It was meant to protect minority religions from interference and repression by the government, starting with the government "establishing" an official, government-supported church.<br />
The early settlers left England mostly on religious grounds. They were being persecuted for being puritans, baptists, methodists, etc. in a place where the Chuch of England was in power. The irony was that, once here, they didn't show religious tolerance to their own people.<br />
I always found it hilarious that Roger Williams and his fellow founders of Rhode Island had been forced out of Massachusetts colony for disagreeing with certain doctrines of his fellow puritans who ran Massachusetts. You would think that after being on the receiving end of that kind of crap in England, the Massachusetts puritans would have been more sympathetic to someone like Williams and his followers!
It was meant to prevent feudalism from entering the U.S., but failed. You see, the founding fathers failed to recognize that money was set up to establish feudalism in the first place. Thomas Jefferson actually saw this and predicted the failure of the constitution, but the U.S. enjoys the facade of thinking the constitution is still in force.
It is meant to protect nincompoops in minority from nincompoops in majority.
From everything I can tell in the history books it was to avoid what our forefathers' left in England, govt sanctioned religious institutions, or religiously-run govt. It's a two-sided coin.
It was clearly intended to protect government from religion. The colonist had fled Europe where religion dominated State, seeking to find a place where they could escape religious oppression. The founders were deeply religious people, who lived, worked, breathed their beliefs, and it would never have occured to them that religion would ever need protection from the state. But it was foremost in their minds that the state needed protection from being dominated by religion.
I value protecting the government from religion vs the contrary. I believe freedom of religion is important, but it already has too great an influence on our political process I think. It has basically hijacked one of the major parties in this country, dominating most issues, and still has a powerful influence on the other.