"the wall of separation between church and state" is probably the most misunderstood phrase in American politics. The phrase comes from a private letter written by Jefferson to the Danbury Baptists. The Baptists of Danbury feared the inclusion of a Constitutional protection for the right of "free exercise of religion" because they interpretted it to mean that the right was government given (that if it was given by government it could also be taken away by government) rather than a G-d given right (which would be inalienable). They wrote a letter to Jefferson about their concern to which Jefferson replied explaining to them that the government would take no role regarding the religious practices of Americans:
"Gentlemen
The affectionate sentiments of esteem & approbation which you are so good as to express towards me, on behalf of the Danbury Baptist association, give me the highest satisfaction. my duties dictate a faithful & zealous pursuit of the interests of my constituents, and in proportion as they are persuaded of my fidelity to those duties, the discharge of them becomes more & more pleasing.
Believing with you that religion is a matter which lies solely between man & his god, that he owes account to none other for his faith or his worship, that the legitimate powers of government reach actions only, and not opinions, 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 and state. Adhering to this expression of the supreme will of the nation in behalf of the rights of conscience, I shall see with sincere satisfaction the progress of those sentiments which tend to restore to man all his natural rights, convinced he has no natural right in opposition to his social duties.
I reciprocate your kind prayers for the protection and blessing of the common Father and creator of man, and tender you for yourselves and your religious association, assurances of my high respect & esteem.
Thomas Jefferson
January 1, 1802."
The purpose of Jefferson using this phrase in his letter was to guarantee the right of Americans to practice their faith, not to suppress it! What happened was in 1947 a Justice of the Supreme Court Hugo Black (a Klansman from Alabama who hated Catholics as much if not more than blacks) borrowed and butchered Jefferson's letter to make prayer in public schools illegal.
The best book to read on this subject is "Original Intent: the Courts, the Constitution, and Religion" by David Barton. You can get it on Amazon.com. I had it as a textbook in College and it was honestly one of the best books I've read on American history I highly recommend it.
Amazon has the first 29 pages available online:
http://www.amazon.com/gp/reader/0925279501/ref=sib_dp_bod_ex/105-1793419-0990004?ie=UTF8&p=S003#reader-link