Two quick points:
(1) I may have said this before; I can't remember. In any event, I think perhaps the single goofiest argument for atheism is when they list some implications of the existence of God (whether it's his allowance of the Holocaust or whatever), and then conclude, "I don't want to believe in a God like that."
They say this with self-righteous huffery, as if they've just blown up their silly theist opponent. In any other argument, this would be such a childish stunt that it wouldn't even occur to anyone to try it. "You think if the US hadn't entered World War I, then Hitler wouldn't have come to power!?! Well I don't want to believe in a historical narrative like that. QED."
(2) The Catholic Church has been responsible for some terrible stuff, I grant you that. (BTW I was raised Catholic but am no longer one; I'm simply trying to correct a common simplification.) And then there's all the Galileo stuff; maybe Gene can give us a good link as to why the typical Dawkins-esque story here is wrong too. But I bet a lot of people don't know where the term "devil's advocate" comes from. It's from the old Church practice of appointing someone to argue against canonization, to make sure the nominee was deserving.