http://www.conservativeusa.org/vareligiousfreedom.htmnote that this is on a conservative site, although it's listed in many other places. It's pretty much a necessary read, and was the precursor to the Establishment Clause in the First Amendment.
Anyway, Jefferson, who was not really religious at all, but did have to make some mention of God back in those days, wrote the statute, and Madison got it passed thorugh the Virginia legislature.
The Founders, at least the important ones, were personally familiar with the religious wars on Europe, and knew what would happen if established religion was instituted here.
It's pretty much what is happening with those who want to establish it-- a huge, artificial divide is being set up, and they would be perfectly happy if it lead to war.