Approximately a third of the passengers on the Mayflower were Puritan Separatists who sought to detach from the established Church of England and to create a society in accordance with their own religious ideals. The early North American colonies were intolerant of religious dissent. They mistakenly chose to perpetuate what they had rejected in England.
However, between the early settlers and the time of the founding there was a maturation. The First Amendment, ratified in 1791 stated that "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof." The phrase "separation of church and state" did not appear in the Constitution. It came later in a letter written by Thomas Jefferson to the Danbury Baptist Association in 1802. In the letter he utilized the phrase a “wall of separation between church and state,” Jefferson, a man of deep religious conviction, believed firmly that religion was a personal matter. He rejected the notion that government should interfere with people’s expression of religious conscience.
Jefferson and the rest of the founding fathers recognized that an established religion was at odds with the freedom they sought to maximize. By instantiating a separation, they removed the incentives for religious competition and created harmony.
Read our favorite quotes: Founding Fathers Quotes on Religious Freedom and the Separation Between Church & State at Ammo.com