First, about Kennedy, real quick. Just because the government says that you can't stop a man from running for president based on his religion, they DO NOT SAY that you can't use that as a reson to vote against him. Would you vote for a devil worshipper (even if he swore he would not let his religion influence him)? Would you vote for a man who believed that God was a puple elephant that farted-out the world, and was a religion of one? It's your right to consider religion in your decision.
[The rest is more about what the first answer guy wrote.]
Number one, I think that people have a right to be protected FROM religion. (you are right, all of the Bill of Rights is about protecting people from bad things, including oppessive religion, and the government, but it is not about protecting the government.)
Number two, I think that the government should be protected form and isolated from religion. (This has more or less been interprted over the years, not in the actual Bill of Rights
I don't believe that the founding fathers were worried about protecting religion at all. They had witnessed and fled from a religion that had taken over practically every government on a continent, into some kind of sick, incestuous (ask all the royal hemophiliacs), lethargic, hateful, xenophobic Europe. They called it Popery and they sure as hell didn't want to see the same thing happen here. That is what the clause in question is all about.
I come from the southern coast of Maine. Back during the 1620's-early 1700's our area was a haven for people fleeing the religious indolence of the colonists in Mass. (Ironic because they themselves had fled religious persecution, so you would think that they would be a little more tolerant to people who did not believe EXACTLY what they believed)
So if you try to say that the colonists had a tradition of Christianity going back to the very beginning, then I will say that my people have a tradition, going back to the very beginning, of protecting dissenters from over-bearing, bible-thumping, religious wackos.