Ed Brayton: if Jefferson had wanted religion in government, he'd have put it in the Constitution when he wrote it!

Ed:

[Jefferson] believed that it forbid the government from taking any position at all about religion. When he was president, he refused to issue even purely advisory declarations of prayer and thanksgiving, something both of his predecessors had done.

Important point, if it had any relevance to the Constitution, which it doesn't.

Jefferson had nothing to do with the drafting or ratifying of the Constitution--he was in Europe during the debate and ratification.

The term "separation of church and state" dates to the 17th century, and was in common parlance during debate and ratification of the Constitution. Except that the term was never used in the debate, according to the minutes of the debate. The Constitutional Congress was fully aware of the concept of separation of church and state, and thought it so irrelevant to Constitutional law that not a single member of the Congress used it on record in the debate.

From my own post a while back:

"[S]eparation of church and state" was first used publicly in America not by Thomas Jefferson but by Roger Williams In Rhode Island in 1644, and was widely discussed prior to ratification of the Constitution in 1789 (most prominently by Madison). Despite extensive public discussion of "separation of church and state" and its implications, or more accurately because of the discussion and its implications, "separation of church and state" was not mentioned even once in the Congressional record from June 7 to September 25 during the Founders' recorded official debate on the First Amendment in 1789. 

"Separation" was a well-known and vigorously debated concept for 150 years prior to the Constitutional Convention, and was discredited. The separation phrase was debated vigorously and extensively before the Constitutional convention, and "separators" lost the debate so decisively that the phrase wasn't even mentioned in the Convention, let alone in the Constitution.

So how did "separation of church and state" get into Constitutional law? It was put there by a KKK Kleagle--the former Klansman and Kleagle for Klan recruitment in Alabama in the 1920's named Hugo Black, who was put on the Supreme Court by FDR as a payback for Black's support for his New Deal legislation in the 1930's. The Klan was a crucial cog in the Democrat coalition, and "separation of church and state" was a part of the Alabama Klan initiation oath the Black administered for years to new Klan recruits (it was designed to prevent government support of Catholic schools).

I describe Hugo Black's career and the provenance of "separation of church and state" in detail here.

So while Jefferson had nothing whatsoever to do with the Constitution, and his musing in private letters has nothing genuinely to do with Constitutional law, Jefferson did have strong views on the origin of our rights as Americans:

We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.--That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed, --That whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it, and to institute new Government...

Jefferson noted that our rights come from our Creator.

He also noted that the government derives its just powers from the consent of the governed, and that it is the right of the People to alter or abolish it when Government becomes destructive of its rightful ends.

We're getting there.