It cannot make the US a religious free zone, but it does guarantee that religious laws cannot be imposed on non-believers. The establishment clause also means a lot more than simply disallowing the state from endorsing a single state religion. The establishment that it prohibits can also include effective and constructive establishment.
See, that's not right. If they believe in Martians, then they're probably dumb or nuts. We've examined Mars in great detail, and there's no one there. And that's why I certainly would respect the intelligence of an atheist over a theist, because the evidence against deities is tremendous. Someone who made real decisions about policy based on what he or she perceived as god handing out orders would bother me immensely, because that's kinda nuts to me. Bush defended the war in Iraq, back in 2004, by saying that he thought god had told him to bring freedom to Middle Eastern nations. Several of the Republican candidates in 2008 said that they believed that god had commanded them to run. Sure, some of them were just using religious rhetoric to pander for votes, but the ones that actually believe that there's a bearded old man up there who is taking an active part in our politics is scary. Paul Broun, a Georgia congressman, is on the House Committee on Science, Space and Technology, and condemns a lot of modern biology as "lies from the pit of hell". That scares me, a lot. I don't see how a person who thinks that science is a tool by an evil satyr to trick people is qualified to make decisions about laws pertaining to science. Just like I don't see how a person who thinks that god maintains the world in a constant state is qualified to make decisions about the environment or climate change. I don't see how a person who thinks that their religion requires them to conduct a holy war on Islam is qualified to be commander in chief, either.
Leaders who actually think this stuff is true are very dangerous and should not be elected into office. Obviously, I'm not saying they should be legally prevented from running because of it, but they should be laughed out of the race, because they are nuts and are dangerous. And so we should care what they believe. We shouldn't elect conspiracy theorists either. Or lots of people who believe crazy things.