{No spoilers} You might not expect a comic book movie to delve into one of mankind's oldest and most fundamental philosophical questions, but Batman v. Superman does just that by utilizing Lex Luthor to ask about how an all powerful and all good God can co-exist with evil/tragedy in our world. In theology, we call this theodicy, or The Problem of Evil. Evil, both human caused and natural (disasters/disease/death) does indeed exist, only a fool would try to call the inhumanity of man toward his fellow man anything but evil, and only someone who is heartless would not be troubled by the latest drought/plague/volcano, etc. to spread misery and destruction. Lux Luthor, played by Jesse Eisenberg, shares his belief that God cannot be both all powerful and all good, a conclusion that apparently contributed to his path toward villainy, an assertion that is not met with a response, per se, by any of the movie's heroes apart from their subsequent self-sacrificial actions. In the movie, Superman's motives and choices are called into question, because of his power, as characters wonder if Superman must save everyone who is in danger, and if he doesn't, is he responsible for that 'neglect'? Bruce Wayne/Batman does indeed hold Superman at least partly responsible for the destruction caused in his efforts to fight evil {General Zod from the last Superman movie}.
So, what is the Christian response to the problem of evil? There are three possible choices: (1) Emphasize the sovereignty of God, as typified by the book of Job, with a "who are you to question God?" response, (2) emphasize the freewill of humanity, as typified by the German philosopher Gottfried Leibniz, who maintained that this is the best of all possible worlds that God could have created because human freewill with its accompanying evil is better than a world of automatons, (3) or attempt to meld some combination of God's sovereignty and human freewill.
A foundational belief that is built into Christian theology, which also has a significant impact upon theodicy, is Original Sin. The idea that the world was created without flaws, humanity included, but that both humanity and the world around us (i.e. disease, natural disasters, etc.) are consequences of humanity's rebellion against God. The finale of Christian theology, the End Times, as expounded primarily in Revelation, also posits that God will do away with this world, making a new heaven and new earth, one that is free of these causes of pain and suffering, at the same time that he removes the stain of sin, for good, from humanity.
Another aspect of the Christian response to the problem of evil is to consider the relationship between God and humanity within the analogy of parenting. God often refers to himself in parental terms. We know full well the warping danger of withholding consequences from our children, some of whom would become spoiled brats given that level of intervention, others of which would be psychopaths. God must allow humanity to taste the bitterness of rebellion, of independence from him, if only to allow us to learn the value of obedience.
In the end, the problem of evil isn't going away any more than evil itself. It will still cause skeptics to doubt God, it will still trouble believers (as it should), but the ultimate answer remains the same: Choose to trust in the goodness of God.