I'm a devout Roman Catholic, but I have absolutely nothing against atheists/agnostics. To each his own. My only problem is with the loons that think that religion is the root of all evil and will destroy us all (even though we've had it for about, oh, thousands upon thousands of years) and want to see it completely banned. Hell, I've even seen some call for the persecution of the religious (I assume most of them are trolling, though), which just strikes me as ironic in a sad way.
Religion in itself is not evil. I think the moral teachings of Jesus Christ ("Do good to those who hate you", "Love thy neighbor as thyself", etc.) are something that every decent human being can agree on, even if they disagree about Christ's divinity.
No, it's not religion, it's when people use religion to get what they want. It's people who use religion to gain power and wealth that are the problem, not religion itself.