Someone correct me if I'm wrong: The "founding fathers" were Protestants for the most part and I doubt that they had Muslim, Buddhists, and pagans on their mind when they instituted the First Amendment. I think the intention was more towards protecting Protestants. Now, obviously, it's worked out for the greater good, so I'm not saying it's a bad thing.
Another thing: Isn't the seperation of Church and State intended so that the State doesn't become a theocracy? I recall hearing that there was some sort of issue with a state government somewhere loaning a church money and some people got incensed over it.