Nah, religion is mostly harmless. There's scientology of course, and crusades, and jihadists, but the rest of it is ok. I wouldn't mind going after people who kill for their religions, or kill other people because of their religions (i.e. Bush's crusade against the evil Muslims, or the jihadist crusade against the evil infidels, or the Scientologist policy of "fair game"). That's wrong when it's done for secular reasons, it's wrong when it's done for religious reasons, it's wrong any way you look at it, and those who do it should be stopped. Provided you're not killing people or anything, you should be allowed to believe whatever you want to believe.
I do think a good government would be likely to have only atheists in it, but I don't exclude the possibility that some theists could be equally good rulers, nor do I assume that all atheists would be good rulers. The idea of restricting a government to atheists only is silly, and unlikely to improve anything. However, I do think we should have much higher standards for who is allowed to make decisions on behalf of the country. At present, you could be a high school dropout who thinks the Earth is flat and babies are delivered by storks, just so long as you have enough money to support a massive propaganda campaign. When/if you do that, you get to pass laws about what is or is not to be included in school education. It doesn't make any sense. Even worse is that most laws aren't even read before they're passed. The system is broken.