There is a lot of confusion of Sep of Church and State vs. Freedom of Religion (not from religion).
The 1st amendment gives freedom OF religion, which means that everyone can freely practice their own religion. The state will not have a mandatory religion that they enforce upon everyone. The free practice of your religion will not be infringed upon. This is not freedom from religion, this does not mean that a politician can't be religious or a public school teacher can't talk about their religion, in fact preventing them from doing so does infringe upon their free practice of their religion.
So where does separation of church and state come in? It wasn't in any founding document. The term is first used by Thomas Jefferson in a letter to Connecticut Baptists.
The phrase "separation between church & state" is generally traced to a January 1, 1802 letter by Thomas Jefferson, addressed to the Danbury Baptist Association in Connecticut, and published in a Massachusetts newspaper. Jefferson wrote,
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"I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion, or prohibiting the free exercise thereof,' thus building a wall of separation between Church & State."[1]
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Jefferson was echoing the language of the founder of the first Baptist church in America, Roger Williams who had written in 1644,
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"[A] hedge or wall of separation between the garden of the church and the wilderness of the world."
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This has been used as an argument in the Supreme court throughout the years to look at the 1st amendment differently than it is really written.
Jefferson's metaphor of a wall of separation has been cited repeatedly by the U.S. Supreme Court. In Reynolds v. United States (1879) the Court wrote that Jefferson's comments "may be accepted almost as an authoritative declaration of the scope and effect of the [First] Amendment." In Everson v. Board of Education (1947), Justice Hugo Black wrote: "In the words of Thomas Jefferson, the clause against establishment of religion by law was intended to erect a wall of separation between church and state."[2]
However, the Court has not always interpreted the constitutional principle as absolute, and the proper extent of separation between government and religion in the U.S. remains an ongoing subject of impassioned debate.[3][4][5][6]
I tend to be on the side that believes everyone should be allowed to freely practice their religion. If a teacher wishes to lead a group of christian students in prayer they should be able to, a muslim teacher can do the same. No student should be forced to participate in practices they are not comfortable with. I believe in freedom of religion the state shouldn't be able to tell someone they can't practice or express their religion. Nor should the state impose any religion. I think it is dubious to take one letter from one founder and to color the entire 1st amendment with it. I disagree with Jefferson on many things and it is unfortunate that this has become a principle in our country when it in no way is in any of our founding documents.