Unfortunately part of the problem is that we were kinda-sorta-but-not-articulately founded on the concept of religious freedom, but certainly not on religious pluralism. On this subject, you could probably count the founding fathers in two categories:
The intellectuals, such as Benjamin Franklin and Thomas Jefferson, who meant what they said. (Jefferson's gravestone epitaph lists the three things he was proudest of: the Declaration of Independence, founding the University of Virginia, and author of the Statute of Virginia for Religious Freedom. Franklin was an avowed deist.)
The rest of them, who were far more worked up about the King's role as head of the Church of England. For them, religious freedom meant freedom from governmental control of Christianity; Christian control of the government wasn't altogether offensive.
That's one of the wacky things I love about this country; the schizophrenic split between the rustic Puritan influence and intellectual liberalism was there at the founding and survives today.