For 1500 years, starting around year 400, individual kingdoms in Europe struggled with Rome's church over laws, power and taxes. The religious (and political) rule of the Catholic church was engrained into most every kingdom of Europe, directly affecting individual religious freedoms throughout Europe.
In part, because of these conflicts, and in part due to the internal politics of Rome's church, new churches were founded, based on Roman church beliefs, but separated from Rome. These new churches were founded "in protest", and became to be known as "Protestant Faiths".
In 1534, and shortly after the Spanish discovery of a new world, England wholly split from Rome's Catholic church (note 1). However, for the people of England, one religious tyranny was simply replaced by another. As the newly established Church of England took the same place the Catholic Church previously held.
In 1562, the French kicked off colonisation efforts within what would later become the "thirteen colonies". In 1607, with the landing at Jamestown, England started thier colonization efforts of the new world (note 2).
In the earliest history of colonization by Europeans, protestant groups fled to join communities where they could follow thier individual religious beliefs. Most of these people were fleeing from governments that mandated a specific (usually Catholic) religious belief. So, they went to this new, sparsely populated land and established individual settlements where they could follow their own beliefs.
As the British Empire took a firm hold on the colonies, the freedom of the new world began to erode. In 1706, South Carolina established the Anglican Church (the Church of England) as the official church of the colony.
Taxes became a larger problem than religion, and ultimately, it was money that led to the American Revolution. However, the religious roots of the new world were not forgotten.
Thomas Jefferson wrote the original "Rough Draft" for the Declaration of Independence. Several changes were made to the document, before it was ratified, and read publicly. The Constitution of the United States, and the original Bill of Rights (the original 10 amendments to the constitution) were both written by James Madison. Thomas Jefferson was a friend of Madison, but was not directly involved in its creation.
Jefferson is quoted as saying, in one of his letters, "wall of separation between church and state." Which he believed when he wrote the letter in 1801, was guaranteed by the first amendment to the constitution.
To whom did he send this letter, and why?
It was to a group of Baptists. They were seeking relief from the rules imposed by more established religions within Connecticut. These protestants were the first to demand neutrality from the government in religious matters. However, the idea of separation of church and state was so foreign to them that they dismissed the letter, and sought relief through other means.
So, while the phrase is commonly attributed (note 3*) to Thomas Jefferson, it was not codified into law within Jefferson's lifetime. It's not part of the bill of rights, or the constitution.
The popularity of "Separation of Church and State" has grown and diminished throughout this country's short history (note 4). In 1878, the US Supreme Court accepted Jefferson's "Wall of Separation". However, they did so, to keep Mormons from using the First Amendment's protections to escape prosecution for polygamy. The court decided that the Government and it's laws are written to regulate actions and not opinions.
In 1947, the Supreme Court again used Jefferson's "Wall of Separation" letter to clarify it's definition. This time stating that the wall of separation is the cornerstone of the first ammendment. In this they agreed that a religious entity cannot be excluded benefits from a law or program that benefits the population as a whole (note 5).
Now that the original ills that brought the need for a separation of church and state to the forefront are an almost forgotten piece of history, the tenet has become a symbol of forced government tolerance of everything that originated as a religous code.
However, in it's use, the Supreme Court has never crossed the original stand; "laws are written to regulate actions". Even in the 2003 overturning of a Texas anti-sodomy law, the arguments were made invalid on the guarantee of the Fourth Amendment (search and seizure), not on the First Amendment's "anti establishment" clause.
Note 1: While Divorce was a factor in Henry VIII's decision, Catholic governance and taxes had already, long been a contentious issue throughout Europe (not just England).
Note 2: Charles Fort was established by French Hugonauts (protestants)
seeking religious freedom from the Catholic Church in France. Jamestown
was a business endeavor, and the first recorded African slave trade within
North America happened here in 1619. In the scheme of things, Jamestown
was the exception for settlements in this region.
Note 3: Steve Edenbo, who is uniquely in the know, sent me an Email. My original text said "phrase originated from". Steve said,
When he penned that phrase on New Year's Day of 1802, to the Danbury Baptists, he was referencing a quote of Roger Williams, one of the founders of Rhode Island, and one of the originators of complete religious freedom in America. The quote of Williams is:I say, thank you, Steve."When they have opened a gap in the hedge or wall of separation between the garden of the church and the wilderness of the world, God hath ever broke down the wall itself, ... and made His Garden a wilderness as it is this day." (from Williams' Mr. Cotton's Letter Lately Printed, Examined, and Answered, 1644)I first found this quote of Roger Williams on the following web page http://www.twelvetribes.com/publications/separation-church-state.html, which is interesting primarily due to its excellent footnotes, pointing to hardcopy books available in libraries.
Note 4: Some Historians, such as Philip Hamburger, attribute the general acceptance of the tenet to 19th century Anti-Catholic religious movements, including the Ku Klux Klan and Free Masons. These and other movements lobbied for the importance of the tenet in response to the Catholic Church formally denounced "Separation of Church and State" (meaning the separation of a state from Catholic rule) in 1832.
Note 5: Search as I might, I cannot find another case where the 'separation of church and state' was explicitly used by the supreme court.