"The purpose of separation of church and state is to keep forever from these shores the ceaseless strife that has soaked the soil of Europe in blood for centuries." -- James Madison, 1803
What do you think Madison meant by that? Was he concerned that (A) religious people would be persecuted or, (B) the 'Church', like they did in Europe 'for centuries', would 'soak the soil with the blood' of those who didn't adhere?
If you answered 'A', you're ignorant of history and don't know the facts laid out in the U.S. Constitution by the Founders and Framers of this country. If you answered 'B', you get it.
"Strongly guarded as is the separation between Religion & Govt in the Constitution of the United States the danger of encroachment by Ecclesiastical Bodies, may be illustrated by precedents already furnished in their short history [ttempts where religious bodies had already tried to encroach on the government]." -- James Madison, Detached Memoranda, 1820
"Ecclesiastical establishments tend to great ignorance and corruption, all of which facilitate the execution of mischievous projects." -- James Madison, letter to William Bradford, Jr., January 1774
The Constitution protects the American people from religion, not the other way around.
And that's from the man who wrote it.