This is, of course, the classic Problem of Evil. And it certainly comes to mind after an attack like this. It is, it seems to me, contra D'Souza, a far bigger problem for theism than the lack of comfort is for atheism.
Following in the footsteps of centureis of theologians, D'Souza takes his own whack at the Problem of Evil. His words must be read to be believed:
This is a deep question about God's hiddenness in the world. Why doesn't God make himself manifest, especially when there is tragedy to be averted? Here's one possible reason. Imagine if there was divine intervention to prevent Cho from doing what he did. Leave aside the issue of what happens to human free will. Just focus on the consequences. Cho would have been--let us say by miraculous intrusion--disarmed, the shootings would have been prevented, and life would go on.
In short, life would proceed as if God had not intervened in the first place. So God in this view becomes a kind of cosmic errand boy, who is supposed to do our chores and clean up our messes and we then wish him a very good day and return to our everyday lives. But perhaps God's purpose in the world (I am only thinking aloud here) is to draw his creatures to him. And you have to admit that tragedies like this one at Virginia Tech help to do that!
Now, I would dispute the notion that a God who intervened to stop evil acts like this would be an errand boy -- he would be more like Superman, whom we all admire.
But think about D'Souza's claim here: God allowed this attack in order to "draw his creatures [that is, us] to him." If you accept this view, then Cho isn't really evil is he? After all, he did God's work by drawing us closer to him! And the folks whom he killed are all frolicking in the Magic Kingdom anyway, so what's the harm?
What kind of God would allow more than thirty people to be murdered in order to "draw his creatures to him"? D'Souza's deity is about as kind, loving, and moral as the villain in the movie Saw, who tortures and murders people, supposedly in order to make them appreciate life more. Imagine telling the parent of a twenty-year-old college student that God let Cho murder your son or daughter in order to draw you closer to him?
Couldn't God use a burning bush, or maybe a vision on the road to Richmond, or even really vivid dreams? Did he have to use mass murder to further his purposes? D'Souza posits the eixstence of a sadistic psychopath with omnipotent powers. What comfort!
UPDATE: PZ Myers takes D'Souza's theology to its logical extreme: He's going to take a ball peen hammer to the cats in order to unite his family in love. (Note to the irony-impaired: he doesn't actually plan to do this. Rather, it's an example of where D'Souza's theology leads.)