It’s important to note that Jefferson did not play a direct role in the writing of the Constitution. He was in France when it was drafted in 1787. He was stateside in 1791 when the Bill of Rights (the first ten amendments to the Constitution) were being written, but he was not in the Congress at the time, nor directly involved. However, one could argue that through his friendship with James Madison, a key figure in writing the Bill of Rights, Jefferson at least played an indirect role in helping to fashion them.
The whole notion of the separation of church and state (even the wording) gets back, we are told, to Thomas Jefferson. In 1947, in the case of Everson vs. the Board of Education, the U. S. Supreme Court made a ruling in which they applied Jefferson’s phrase “the separation of church and state” to the meaning of the establishment clause.
Because of a misunderstanding about “the separation of church and state,” all sorts of terrible things happening against Christians today. This is not what the founders intended, certainly not Thomas Jefferson. The founders (including Thomas Jefferson) believed that religion—by which they meant Christianity—should be voluntary and should be allowed to flourish in the public arena. There is no way they would agree with the anti-Christian crusade that has been taking place lately—to try to scrub the public arena of any vestige of Christian expression in the public arena.
Many conservative critics note that the separation was meant as a garden wall protecting the church from any intrusion from the state so that it would grow and flourish unhindered by laws and ordinances of the state. The devout William Penn has writings to this effect.
 Of course, one could argue that the separation of the institution of the church and of the state can be found in the Bible itself. For example, there was a distinct separation of the king from the temple and religious duties. See Exodus 30:1-10. 2 Chronicles 26:16-20 describes a situation where the king was punished severely by God for overstepping his regal authority and taking on priestly duties.