But in case you are asking more than why the exact phrase "Separation Of Church and State" doesn't appear in the constitution, I'll throw you a bone. This article says it better than I can-
Much misinformation about the history behind separation of church and state may be traced to David Barton, a Texas-based propagandist who attacks separation of church and state in books and videos. Barton's materials contain numerous errors, distortions and half truths. His book The Myth of Separation, although heavily footnoted, is riddled with factual errors. Nevertheless, Barton's revisionist history is appearing with increasing frequency in Far Right circles and is leaching into the secular media by right-wing activists who write letters to the editor and op-ed columns regurgitating Barton's bad history.

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MYTH: Separation of church and state is not in the U.S. Constitution.

It is true that the literal phrase "separation of church and state" does not appear in the Constitution, but that does not mean the concept isn't there. The First Amendment says "Congress shall make no law respecting an establishment of religion or prohibiting the free exercise thereof...."

What does that mean? A little history is helpful: In an 1802 letter to the Danbury (Conn.) Baptist Association, the-president Thomas Jefferson declared that the American people through the First Amendment had erected a "wall of separation between church and state," echoing religious freedom advocate Roger Williams who a century earlier alluded to the "hedge or wall of separation between the garden of the church and the wilderness of the world."

James Madison, considered to be the Father of the Constitution and author of the First Amendment, said in an 1819 letter, "he number, the industry and the morality of the priesthood, and the devotion of the people have been manifestly increased by the total separation of the church and state." In an earlier, undated essay (probably early 1800s), Madison wrote, "Strongly guarded...is the separation between religion and government in the Constitution of the United States."

As eminent church-state scholar Leo Pfeffer notes in his book, Church, State and Freedom, "It is true, of course, that the phrase 'separation of church and state' does not appear in the Constitution. But it was inevitable that some convenient term should come into existence to verbalize a principle so clearly and widely held by the American people....he right to a fair trial is generally accepted to be a constitutional principle; yet the term 'fair trial' is not found in the Constitution. To bring the point even closer home, who would deny that 'religious liberty' is a constitutional principle? Yet that phrase too is not in the Constitution. The universal acceptance which all these terms, including 'separation of church and state,' have received in America would seem to confirm rather than disparage their reality as basic American democratic principles."

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(the author of the preceeding work has granted full permission to reproduce in whole or in part:
Rob Boston
Americans United for Separation of Church and State
Silver Spring, Maryland
[link|http://www.geocities.com/Tokyo/Temple/9917/ffc/badconstitution.html|http://www.geocities...constitution.html]


A copy of the original piece (the author's yahoo link is dead) can be found [link|http://bartcopnation.com/dc/dcboard.php?az=show_mesg&forum=8&topic_id=3&mesg_id=3&page=6|here]