No doubt one of the strongest arguments against the major religious faiths goes like this: If God is omnipotent, then why does He allow so much suffering? E.g. a bunch of people emailed me after my religious LRC articles and wanted to know why "your loving God allowed the Holocaust!"
I've spent a lot of time thinking about this, but (as you may guess) there are many different issues involved and one could write books on it. Rather than do nothing, however, let me give a snapshot of my current view. Naturally this blog post won't convince an atheist, but it may resonate with believers who haven't known what to do with this challenge.
First, let's acknowledge that it is a problem. For Bible-believing Christians (or orthodox Jews), it's even worse. Not only does God allow humans to do evil things, He even (in the Old Testament) ordered the Israelites to slaughter infants. Whoa!
Nonetheless (for the believer), there has to be an explanation. For Christians, we know this quite easily: Jesus certainly felt that the Father was holy and moral, and Jesus certainly knew the scriptures and what had happened in the past.
Now here's where I simply hope that the reader has had experiences like mine: Have you ever thought a person's behavior was totally inexplicable, but then as you learned more of the situation, it became a lot more coherent? Indeed, have you ever thought back, say, to kids you knew in high school (or whenever) and hated at the time, but now you realize they were right and their scoffers (including you at the time) were dead wrong?
Or try this route: I don't care who you pick, be it Adolf Hitler, a serial killer, or George Bush (if that's your politics): If you watched a movie of this person's life, by the time he did the horrible things, you would totally understand and expect it. I.e. in the context of this person's experiences, his behavior would make perfect sense. It's not as if you'd be shocked at the serial killer's first murder, if you had seen a history of his life up till that moment. (Don't be thrown too much by the analogy; I'm not saying you would think these people did the right thing at the time, just that you'd totally understand why.)
Okay: When it comes to understanding the motives for God's actions, the relevant history is, all of time. So if you can see that humility should make you reserve judgment on people because you didn't know all the facts, can you possibly imagine what sorts of considerations God makes when deciding what to do??
Conclusion: If you are a Christian, when you die you will be in paradise. And one aspect of that is that you will fully comprehend--and totally agree that it was the most moral thing to do--why God ordered the Israelites to sack entire cities, why He didn't zap Hitler with a lightning bolt, etc. Granted, I have no idea how some things are going to make sense, but that's part of the excitement for the Christian: Some day it really will make perfect sense; you will realize that God created the best of all possible worlds.