Actually, it was mostly the deists who were behind the seperation of church and state. They didn't want Christians telling them what to believe, and many of them, such as Thomas Jefferson and John Quincy Adams, were distrustful of the church.

Yeah, despite attempts to rewrite history, not all of the founding fathers were Christian. As mentioned, Thomas Jefferson and John Q. Adams weren't. Nor were Benjamin Frankly, Ethan Allen, James Madison, or George Washington. They were deists. They did not believe in the bible, or in churches. Thus, they didn't want the church to be butting into government, telling them what to believe.

Were most of the founding fathers Christian? Yeah. But not all of them, and some of the most influential weren't. Virtually every step of the constitution was paved with comprimise. The northern states wanted to abolish slavery, but the southern states wanted to keep it. So, some states had slavery, some didn't. Some of them wanted democracy. Others wanted a more stable government. So we got representative democracy. Prayer at the beginning of Congress was one of these comprimises. The Christians wanted to kick things off with a prayer, and the deists didn't care to stop them.

But to imply that all of the founding fathers were Christian would be false, just as it would be false to claim that America was founded as a Christian nation. Seperation of church and state was created to protect the infidel from the believer, as much as to protect the believer from the infidel.