Filling in for Michael Totten, Callimachus has written a great piece on the Founding Fathers' views on freedom of religion, and how they apply, or should apply today. He does a great job of making the case for religious toleration, with the limit being that one cannot use religious freedom to subvert religious freedom. Read it. I posted a good comment over there, as did many others. As with all heated discussions, there's troll activity.
Anyway, here's what I said:
In my view, there isn't that big of a difference between what the Founders thought, and what Popper thought. It is clear, and the Founders are correct, that they wanted a nation in which people had freedom of conscience, and of religion. The state could not impose one religion or the other, neither could it oppose one's right to freely exercise that religion. The line is clear, though. You cannot use your religion to actually subvert freedom of religion, or any other rights. You can believe that you should, but you do not have the right to actually act on such a belief.
Radical Islamists, Communists, Nazis, etc. can express any ideas that they want under the First Amendment, as wicked as those ideas are. They cannot use those ideas to justify acts that take away others' rights.
Rape, murder, actual acts of treason, etc. are not protected speech, because they violate others' rights. The answer is to confront evil ideas with good ideas, not outlaw them (regardless of any justifications the much ballyhooed Venona Papers supposedly establish). When ideas turn to action, then it's another matter.
As a matter of principle, I think Popper was simply suggesting that it is philosophically impossible to have unlimited tolerance (a fact that the hardcore multiculturalists haven't understood yet). It becomes problematic ehrn you start using the state to fight intolerance (a possible risk with a lot of European hate crimes laws), because you're back to the same problem again.
At the end of the day, the Founders believed totally in religious toleration, up until the point when it is used to undermine religious toleration (through state power, terrorism, etc). That rule ought to still apply today.