Why doesn't he lift a finger to protect rape victims and abused children? Even I with my "limited comprehension of reality as a human being" can see that that isn't right.
It isn't right because we assume we know what and why God is thinking and doing or not doing. When we assume this, we proceed to demand an explanation.
As a believer myself, I am faced with a greater dilemma than you (a non believer) in trying to reconcile this problem. And the closest I can come to it is the fact that I simply don't comprehend enough. I may never understand enough. But I accept this. I accept that God is a superior being to me and knows or comprehends the issue to a much greater extent than I.
This of course isn't anything new, it's what the scriptures repeatedly state. That we are not the same as God.