Separation of Church and State

I have tried to search for answers, but I mostly find special interest group pages that offer zero explanation behind their ideas.

When people and groups talk about the separation of church and state, are they simply talking about the first ammendment where it says, “Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof”?

To me, this doesn’t really seem to say that religion should be kept out of all government matters.

I agree with separation of church and state for the most part. Are people that complain about things like prayer before inauguration saying that it implies state endorsement of a particular religion, and that this is in a sense establishes an official government religion?

As a general rule, Yes.

The doctrine of the Separation of Church and State (SOCAS)
was included in the bill of Rights as a preventive measure against the sort of religious tyranny in Europe that caused the persecution of dissenters from the Church of England. In England, Quakers were hanged, Catholics were banned from public office, tithing to the Church was enforced by the state, and the Monarch was also the Head of the Church. Our
Founding Fathers wanted to keep the same mischief away from our shores.

In my view, having prayers before the inauguration or having a Congressional chaplain do not violate SOCAS. While our founders were mostly Deist products of the Enlightenment, they did not envision an America utterly alien to religion. When the president professes a personal belief in Jesus Christ as his savior, it does not harm Muslims, Jews, Buddhists, or Wiccans. Now, if Congress passed a tax on all non-Christians, THAT would be a violation of SOCAS. If Congress required that any officeholder must be a Baptist, THAT would violate the First Amendment.

I see no problem with the National Christmas Tree or having menorahs on Federal buildings; they represent a cultural as well as a religious heritage.

Where does the phrase “Separation of Church and State” come from? Is this a recently coined phrase? It seems to me that it obviously implies much more than the first ammendment.

Actually, it would be a violation in the first place of Article VI:

It comes from a letter that Thomas Jefferson wrote to a Baptist Church in Danbury, CT, after they sent him a letter congratulating him on winning the election.
http://lcweb.loc.gov/loc/lcib/9806/danpre.html

To summarize the letter, Jefferson thanks the Danbury Baptists for their congratulations, then states that he agrees with them on religious matters. He says that the First Amendment established a “wall of seperation between Church and State”, and that this was a good thing.