I am a theist, and I would hate for the government to establish a religion. In doing so, the government, not the church, would be the arbiter of what is good and bad doctrine, and that would stifle freedom of conscience. It is as that point when religion would stop being religious and become a way to control people. This has been the case historically--every time a government has established a state religion, it has proved disastrous.
The genius of the American system is that they allow for religion to exist without establishing state religion. Nobody is coerced into endorsing a particular viewpoint and thus creates a forum where all worldviews, secular and religious, can be expressed. This implies that nobody can have freedom from religion. Religion in this type of system is everywhere, and the views are varied.
However, if freedom from religion was the position that was enforced, then nobody would be allowed to express religious viewpoints. This is censorship. It seems that many people would want the government to do is stamp out any and all religious expression, which would in essence be stopping freedom of religion, which is also guaranteed by the US constitution. I don't see how that is any different that establishing a religion. These people in essence want their viewpoint (no religious expression) to be the one endorsed by the government.
So with these things said, seperation of church and state does not mean that religious people cannot express their views in the public forum. It means that the government will not establish an official state religion, and to date, it has not done so.