The theology of mandated/compulsory prayer in public schools is atrocious, its implementation would be worse.

Prayer is not a "to whom it may concern" letter.  Prayer is a conversation with God on the part of those who have a relationship with him, not a magic formula that if said by enough people will cause God rain down blessings on a land.

I write this knowing that a number of my brothers and sisters in Christ, whose motives I am not assuming or judging, will strongly disagree with this assessment of prayer in public schools.  This issue is, however, connected to numerous others respecting the separation of Church and State, the impact of politics and political tactics upon the Church, and our intended role as Christians first and Americans second.

Note: I put the word compulsory in the title alongside mandated because any practical application of mandating that prayer must be administered by public schools would naturally entail a compulsory element to force compliance upon the schools themselves (the most likely thing being the threat to withhold federal education funding) and the students (detentions, expulsions for those who refuse?).

Why is mandated/compulsory prayer in our public schools such a bad idea?

1. Prayer is already in public schools, each time a teacher or student chooses to pray.

Contrary to what you may have heard, prayer in schools (or anywhere else) has never been illegal.  How could it be?  Prayer is a conversation between yourself and God, one that nobody else is privy to, nor able to control.  In addition to the continued availability of private prayer, prayer that is student initiated and student led (See You At the Pole for example) has always been, and will remain perfectly legal.  {No, having a student lead a prayer over the loudspeaker while students are required to be quiet and listen is not the same thing}

2. We have no need to be led in prayer.

I'm not talking about corporate worship, when the people of God are gathered together and one person leads either a pre-written or spontaneous prayer, as that individual (pastor or otherwise) is acting as a spokesperson for us and focusing our group prayer in one direction; we are praying with him/her, they're not praying on our behalf; that's an important distinction.  With that caveat in place, it is absolutely clear in Scripture that because of the nature of the New Covenant, with Jesus serving as our mediator, that we can approach God directly in prayer.  We have direct access to the Father. 

Ephesians 3:12 New International Version

In him and through faith in him we may approach God with freedom and confidence.

Hebrews 4:16 New International Version

Let us then approach God’s throne of grace with confidence, so that we may receive mercy and find grace to help us in our time of need.

Romans 8:14-15 New International Version

For those who are led by the Spirit of God are the children of God. 15 The Spirit you received does not make you slaves, so that you live in fear again; rather, the Spirit you received brought about your adoption to sonship. And by him we cry, “Abba, Father.”

3. Rote, compelled, and thus insincere prayer (like worship) is not only not honoring to God, it actually offends and angers God.

What would mandated/compulsory prayer in public schools actually be?  Would it be sincere acts of worship?  How could it be for the millions of school children (and teachers) told to pray to a God in whom they do not believe, or told to pray in a way contrary to the dictates of their conscience?  How could these prayers possibly be genuine and from the heart?  What they would actually be is a repeated affront to God, as if God is compelled to bless our nation because we've required everyone to pray, as if God is beholden to us, and not the other way around.  God will not be manipulated, and God will not be mocked.

Jeremiah 7:9-11 New International Version

“‘Will you steal and murder, commit adultery and perjury, burn incense to Baal and follow other gods you have not known, 10 and then come and stand before me in this house, which bears my Name, and say, “We are safe”—safe to do all these detestable things? 11 Has this house, which bears my Name, become a den of robbers to you? But I have been watching! declares the Lord.

Hosea 6:6 New International Version

For I desire mercy, not sacrifice, and acknowledgment of God rather than burnt offerings.

Isaiah 1:11-15 New International Version

“The multitude of your sacrifices—
    what are they to me?” says the Lord.
“I have more than enough of burnt offerings,
    of rams and the fat of fattened animals;
I have no pleasure
    in the blood of bulls and lambs and goats.
12 When you come to appear before me,
    who has asked this of you,
    this trampling of my courts?
13 Stop bringing meaningless offerings!
    Your incense is detestable to me.
New Moons, Sabbaths and convocations—
    I cannot bear your worthless assemblies.
14 Your New Moon feasts and your appointed festivals
    I hate with all my being.
They have become a burden to me;
    I am weary of bearing them.
15 When you spread out your hands in prayer,
    I hide my eyes from you;
even when you offer many prayers,
    I am not listening.

Your hands are full of blood!

4. Requiring non-Christians to pray a Christian prayer hurts evangelism.

How does evangelism work?  What are the most effective methods for sharing the Good News that Jesus Christ has died for our sins and been raised from the dead for our justification?  An important question, and one studied and debated by those engaging in missions and evangelism both here in America and throughout the world.  The answer to that question is never: force people to read the Bible, pray, and attend church.  Why not?  Because it doesn't work.  Only God can make a planted seed grow, only the Holy Spirit can soften the hard heart of human rebellion.  The only thing that compulsory participation, in a religion that you don't believe in, consistently causes in those it is forced upon, is resentment and anger.  State mandated 'Christian' prayer demonstrates to Muslims, Hindus, or Atheists that we do not respect them as Americans, let alone as human beings, how exactly are we creating an opportunity for them to hear the Gospel?

5. A one-size-fits all prayer to God(s) that tries to please everybody, is the most likely outcome.

The last thing I want is a politician or a government employee writing the prayers that our children are required to listen to, and/or recite.  A prayer not directed at God the Father, God the Son, and God the Holy Spirit is not a Christian prayer.  What kind of prayer would we be talking about?  It would have to be one mandated/written by the Federal government at the Department of Education, and thus one designed to please Christians, Muslims, Jews, Hindus, Buddhists, Mormons, Agnostics, Atheists, and thus equally offensive to all and pleasing to nobody.  I absolutely believe in intra-faith prayer, Protestants, Catholics, and Orthodox Christians can and should pray together.  I absolutely do NOT believe in inter-faith prayer, for how can we pray together when we don't agree upon who we're praying to?

6. Focus on prayer in schools is thinking like an American 1st, a Christian 2nd.

This may be hard for some to accept, but as a Christian my citizenship is in Heaven.  That I am an American, while being an honor and a blessing for which I give thanks and a responsibility that carries with it civic duties that I take very seriously, is still in the end, only incidental compared to knowing that my soul has been redeemed by the Blood of the Lamb.  As such, I must always consider what is right in God's eyes, what is beneficial to the Church and its mission to share the Gospel, before considering what I think is right for America.  Often the two are compatible, but there is a divergence more often than many of us are willing to admit.  For example: It may benefit (at least in the short-term) America to 'win' at the expense of another nation economically or militarily, but those who live in that land are human beings just like me, created in the image of God, and thus either fellow followers of Jesus Christ, or those in need of the Gospel.  Either way, as a Christian I look at the world, and my nation's place within it, differently when I consider myself a Christian 1st and an American 2nd.  We call this a Christian Worldview, and it is something more Christians need to embrace.  Trying to revitalize Christendom, through official governmental pronouncements and symbols like prayer in schools, is a nation centric-view, not a Christ-centered view.

7. Societies with compulsory Christian behavior were NOT more Christian in their outcomes.

History teaches us, clearly, that requiring Christian behavior like baptisms, church attendance, and public confessions doesn't create the thoroughly Christian society that the outward appearance projects.  This is not a question of public morality, and has nothing to do with marriage, abortion, or other topics where Christian morality is in conflict with a secular viewpoint.  Morality is a different issue that requires a different theological basis.  We have already seen from Isaiah, Jeremiah, and Hosea (which Jesus quotes) that insincere public acts of worship have the opposite affect of what is intended by those who do them or require them.  This is born out by the clear cut examples of Spain following the Reconquista in which the Inquisition utilized threats and torture to force Muslims and Jews to convert to Christianity, and the more recent example of Dietrich Bonhoeffer's Germany, where nearly everyone was a 'Christian', having been baptized at birth, supporting the Church through taxes, and in his words so fooled by "cheap grace" that their unredeemed hearts still enthralled to sin readily swallowed the godless hatred of the Nazis.  Where did the Holocaust occur?  In the heart of 'Christian' Europe, with the help of millions of people who would have claimed that they were Christians.  Are more examples needed?  Calvin's Geneva, where the Church literally ran the town, was not sustainable (and burned heretics at the stake), nor was the Pilgrim's isolated community (Witch Trails being the most well known flaw).  As we have seen time and time again with the Amish, compelled behavior leads to rebellion, even among those who do believe.

8. Our ancestors in the faith died as martyrs to governments that tried to compel them to not worship, or to worship against their conscience; how can we do that to anyone else?

As a Baptist, this is the final nail in the coffin regarding mandated/compulsory prayer in public schools.  The Roman Empire persecuted Christians because they would not worship the Emperor, murdering untold numbers of them, often in purposefully cruel ways.  During the Reformation, and especially during the horrors of the Thirty Years War, Catholics, Lutherans, and Reformed Christians all were willing to persecute the Anabaptists who insistence upon believer baptism (the idea that the Church is not everyone in town, only those who demonstrate genuine faith) offended all sides equally.  Many of them were drowned in rivers, by those claiming to be 'good Christians' in mockery of their embrace of immersion baptism.  Sadly, years later when the Puritans came to America and finally had power over their own society, they immediately began persecuting anyone showing signs of dissent.  The United States of America was a bold social experiment in that at the time it was one of the few nations in the history of the world to not have an official state religion.  More than that, religious tolerance was enshrined in the Bill of Rights, protecting the Church from the State, and the State from the Church.
I find it ironic that many of the same voices crying out for a ban on Sharia Law in the United States (where it is not even a remote possibility with the Muslim population at 1%), and who, correctly, decry the oppression faced by our brothers and sisters in Christ in Muslim countries and in Communist China, will then turn around and call for the shoe to be on the other foot here in America.  The degree of compulsion may not be the same, nor the penalties for stepping out of line, but the idea of mandating religious behavior is.  What is morally wrong in other countries ought to be morally wrong here as well. 

Kids and teachers pray in school every day that the school is in session, when they choose to.  God is not asking us to pretend that America is a Christian nation through insincere public acts, but to transform our families, churches, and communities through deep commitments to righteous living and sustained efforts at evangelism.  What will propel the Church in America forward is not policies foisted upon an unwilling or indifferent public, but sincere worship, servant's hearts, and morally upright living on the part of God's people.  If you want to transform America, start with the Church.

Does God even want state-mandated prayer?

Calls for a return of required prayer in the nation's public schools are common on social media and letters written to the editors of local newspapers.  Some who I would count as valued colleagues and friends are echoing this call.  As the theory goes, this is a key to turning around the American culture and bringing back a golden age of Christendom where America's status as a Christian Nation was unchallenged {A return to a supposed past Golden Age is a common trope in history, one rarely based in reality; a different topic for another time}.  Setting aside the question of whether or not state-mandated prayer in schools would benefit the culture (An assumption made in the argument, but how would one know if it is true: crime rates?  teen pregnancy? drug use?  Would prayer be expected to lower such things by 10%? 50%  With a complex system like a nation/culture, we cannot single out one factor for much of anything because of interconnected cause/effect.), or the Church itself (Was the Church healthier during periods when the population was required {on pain of various penalties} to pay nominal homage to God?  When everyone living in the land was assumed to be a Christian by simple right of birth regardless of any evidence of the Holy Spirit?  Was that marriage of Church/State a healthier Church?), even if we assume that both the nation and the Church would benefit, that there wouldn't be any unintended negative consequences to either, there still remains a fundamental question that is not being sufficiently considered: Does God want state-mandated prayer?
How can we know the mind of God?  A pertinent question, and one that has a simple answer: we can't, unless God chooses to reveal his mind to us, primarily through his revealed Word.  What then does the Word of God say on the subject?  How has God responded in the past to the worship/prayers/sacrifices of those whose hearts are not invested in the act (in other words, unwilling or indifferent participants)?  For rest assured, if prayer was mandated in the schools, there would be millions, likely a majority, of children and teachers who are not enthusiastic supporters of the particular prayer being offered {Certainly not for Jewish, Hindu, Muslim, Buddhist, agnostic, or atheists, as well as those Christians who would disagree with the particular form and/or verbiage of the prayer being offered.}  A sampling of relevant texts of Scripture follows:

Proverbs 28:9 New International Version (NIV)
If anyone turns a deaf ear to my instruction, even their prayers are detestable.

Isaiah 1:13-18 New International Version (NIV)
13 Stop bringing meaningless offerings!
    Your incense is detestable to me.
New Moons, Sabbaths and convocations—
    I cannot bear your worthless assemblies.
14 Your New Moon feasts and your appointed festivals
    I hate with all my being.
They have become a burden to me;
    I am weary of bearing them.
15 When you spread out your hands in prayer,
    I hide my eyes from you;
even when you offer many prayers,
    I am not listening.
Your hands are full of blood!
16 Wash and make yourselves clean.
    Take your evil deeds out of my sight;
    stop doing wrong.
17 Learn to do right; seek justice.
    Defend the oppressed.[a]
Take up the cause of the fatherless;
    plead the case of the widow.
18 “Come now, let us settle the matter,”
    says the Lord.
“Though your sins are like scarlet,
    they shall be as white as snow;
though they are red as crimson,
    they shall be like wool.

Amos 5:21-23 New International Version (NIV)
21 “I hate, I despise your religious festivals;
    your assemblies are a stench to me.
22 Even though you bring me burnt offerings and grain offerings,
    I will not accept them.
Though you bring choice fellowship offerings,
    I will have no regard for them.
23 Away with the noise of your songs!
    I will not listen to the music of your harps.

Malachi 1:6-10 New International Version (NIV)
Breaking Covenant Through Blemished Sacrifices
6 “A son honors his father, and a slave his master. If I am a father, where is the honor due me? If I am a master, where is the respect due me?” says the Lord Almighty.
“It is you priests who show contempt for my name.
“But you ask, ‘How have we shown contempt for your name?’
7 “By offering defiled food on my altar.
“But you ask, ‘How have we defiled you?’
“By saying that the Lord’s table is contemptible. 8 When you offer blind animals for sacrifice, is that not wrong? When you sacrifice lame or diseased animals, is that not wrong? Try offering them to your governor! Would he be pleased with you? Would he accept you?” says the Lord Almighty.
9 “Now plead with God to be gracious to us. With such offerings from your hands, will he accept you?”—says the Lord Almighty.
10 “Oh, that one of you would shut the temple doors, so that you would not light useless fires on my altar! I am not pleased with you,” says the Lord Almighty, “and I will accept no offering from your hands.

Luke 18:9-14 New International Version (NIV)
9 To some who were confident of their own righteousness and looked down on everyone else, Jesus told this parable: 10 “Two men went up to the temple to pray, one a Pharisee and the other a tax collector. 11 The Pharisee stood by himself and prayed: ‘God, I thank you that I am not like other people—robbers, evildoers, adulterers—or even like this tax collector. 12 I fast twice a week and give a tenth of all I get.’
13 “But the tax collector stood at a distance. He would not even look up to heaven, but beat his breast and said, ‘God, have mercy on me, a sinner.’
14 “I tell you that this man, rather than the other, went home justified before God. For all those who exalt themselves will be humbled, and those who humble themselves will be exalted.”

These are not all of the texts of Scripture that reference insincere or tainted prayer/worship/sacrifices, but they will suffice to show the point: God does not desire, nor accept, from even his own people (or at the least, those claiming to be his people) prayer, worship, or sacrifices that do not come from a humble obedient heart.  If then, these unacceptable efforts were not helpful to the people of Israel, nor to the Church, because they were not genuine, how would they be acceptable to God coming from people of other faiths, or no faith, when compelled by the power/authority of the state?  What about those prayers would be pleasing to God?  Is it not as likely, if not more likely, that such disingenuous rote and compulsory prayer would anger God rather than please him?  Is false prayer better than no prayer at all?  The warnings of the Jewish prophets appear to say 'no'.

Two other factors to consider: (1) Any prayer designed by the government for use in public schools would by its very nature, in keeping with the 1st Amendment, be entirely devoid of specific reference to God.  It could not be a prayer to anything other than a generic god, for generic blessings, and generic guidance/help.  It could not mention Jesus, nor reference the Gospel's call for salvation by grace through faith.  It would, by necessity, be a bland prayer.  Would such a prayer be instructive to young people (what exactly would it teach them about the nature of God?) or pleasing to the God whose name and deeds that we do in fact know?  Even if the government were to somehow avoid violating the 1st Amendment while still including reference to Jesus, it would not differentiate the Jesus of the true Apostolic Church from the Jesus spoken of by the Jehovah's Witnesses or Mormons (both of whom speak highly of Jesus, but a Jesus whose nature and work is very different).  How could a prayer be constructed under the limitations that exist (Nobody is advocating for a repeal of the 1st Amendment, so we must consider this call for prayer in schools within that parameter) that would be properly honoring to God?  (2) If a conservative/evangelical inspired government (the only one likely to pursue this course and the background of those calling for a return of prayer to schools) were to impose school prayer, what is to stop a future liberal/secular inspired government from taking that same prayer and making it explicitly multi-faith (for example: replacing "God" with Allah, or Jesus with Buddha, or stating that all names/approaches to God are equally valid.  'O God, whose faces are many, though all people call equally to you...')?  What started out as a 'win' for Christendom could quickly become an exercise in blasphemy that Christian children would be required to participate in.  If then, that prospect causes anxiety, should not we, as Americans, not wish to put that same anxiety upon fellow citizens who happen to be Muslim, Hindu, Buddhists, etc?  Even though I am 100% convinced that there is only one God, and that he has made himself known as Father, Son, and Holy Spirit, that does not mean I would welcome a return to the policies of past eras where people of other, or no, faith were compelled to acknowledge a God whom they do not believe in.  As a Baptist, I naturally look with trepidation upon any government compelling people in the realm of religion, our ancestors in the faith didn't enjoy being on the wrong end of that, and if we ourselves would object, we cannot advocate imposing the same thing upon others {"Do unto others..."}
The same objections to mandated prayer in school apply to mandated Bible classes in school.  As a former English teacher, I can see the value in teaching the Bible as literature (however, this viewpoint would also treat other religious texts like the Qu'ran in the same way; as literature for students to be made aware of as part of a well-rounded education), and the value in history classes of learning about the role of world religions in human history (a huge factor to be sure, to ignore it is to do a dis-service to history), but NOT the value of having public schools attempt to teach Christian theology.  The reasons are the same as above: (1) Any teaching would have to be generic, and thus liable to offend various Christian sects who vary on one point or another from the mainstream (i.e. Baptists being more/less on their own about baptism, any class on the basic of Christian theology would teach the majority viewpoint), (2) and any class set up to be acceptable to conservatives/evangelicals when they are in power could then be switched to one whose curriculum is approved by a liberal/secular government?  Once again, what started as a 'win' for Christendom could quickly turn into the means to advance what the traditional/apostolic Church considers to be heresy.  If the success of an idea depends upon 'our side' remaining in power, and would subsequently become anathema to us if 'our side' were to lose power, then perhaps that idea is best left on the shelf.

From a strategic standpoint, it seems to me that both prayer and Bible classes in the public schools are a bad idea for the Church, even if they are a 'win' for Christendom (a dubious claim at best).  Others will disagree and see these tools as a means for advancing the cause of the Gospel in the face of an increasingly secular society.  They will contend that the potential benefits outweigh the risks.  We can agree to disagree, as Americans we have that right.  The far more important question that is not being given enough consideration is this: Would God be pleased by these efforts, indifferent to them, or angered by them?  If the examples of Scripture are any indication, and since they are the revealed Word of God, and God does not change, they must indeed be instructive for us concerning the mind of God, the most likely response from God is anger, followed by indifference, leaving pleased as the least likely.  Perhaps there is a Bible-based counter-argument in favor of compulsory prayer and Bible education, given the antipathy shown in the Bible itself to fake prayer/worship/sacrifices, it would have to be extremely compelling.