Thought I'd jump in on this:
It's naive to think that religions were the cause of major wars in history. High school history books simplify things to this level, but it's almost completely not the case. SlothMD is right. Religion is often used as a propoganda tool to persuade a population, or as an excuse to justify other motives. It rarely, if ever, has been the real cause of conflict.
For example: the current "War on Terror" is not religiously based. Islam is not at war with Ango-Christianity. The Nightly News may try to claim this to be the case, but it's simply not.
Sorry to burst anyone's world-view.
Finally, I hated religion in Civ 4 and I'm a builder/dove (dove? ...ick). Why... because although I LOVED the idea of religion, founding them, etc... and I loved playing with them at first, I quickly realized that it broke the game. Religion was massively overpowered for the reasons stated above. They never fixed it. I couldn't play the game because I didn't want to just exploit the AI.
(I should note, I never played a mod that re-balanced religion/corporations, which is a pity).
So many people lament the changes to Civ V and say it is "broken" here and "broken" there. The problem is, they ever only cite examples where they used to like to exploit Civ IV. I have heard legitimate complains about Civ V, but they are few and far between, and they have been discussed ad nauseam and will almost certainly be fixed in patches (I hope).
In conclusion, I'm much happier about religion in Civ V when compared to Civ 4.