The interesting thing that I notice is how he makes his arguments. He really doesn't use facts or philosophical arguments (problem of evil, etc). Most of them are jokes, which makes sense in light of the fact that he's a comedian and not a philosopher or theologian. Nevertheless, I think that there's something larger going on here.
I've been reading a number of books and pieces by the new Atheists that have emerged over the last few years, notably Dawkins and Hitchens. Overall, there's an interesting rhetorical trend that we also see in Maher. They don't really use arguments, they just sneer. Dawkins is probably the most philosophical among them and all he can come up with is something like "well, if God exists, then he most be more complex than the universe and you can't explain the origin of one complexity with something more complex." Well, except you can. My parents or my mother alone is more complex than I was when I was a fetus, so, that's non-sense. He then merily goes on to tell us that science explains everything with all the intellectual erudition you might find in a naive 19th century positivist or possibly a 13 year old revolting against his fundamentalist parents. Yes, of course science can explain everything- except order and complexity of the universe, the existence of life, art, morality, the universality of religion, the human need for meaning and our ability to reason about the world- but everything else it's on top of!
But this is what is puzzling to me, why has Atheism taken to arguing in this way? Why does "oh, come on you can't believe in the virgin birth!" work all of a sudden? My instinct is to think that people's perceptions of reality have become so overwhelmingly secular that the claims of supernatural revelation or even natural theology just seem inherently implausible to them.