In the course of the Seventh Day Baptist debate about our affiliation with the Baptist Joint Committee, the BJC's approach to the "establishment clause" of the First Amendment has been a central issue. The "wall of separation" metaphor used by Jefferson has been often cited. Historical context is provided at The Wittenberg Door :
.... Back in 1791, the year the First Amendment was ratified, 9 of the 13 state governments had official, tax-supported churches. Since the amendment was seen as only applying to the federal government, nobody believed that there was any conflict—nobody, that is, except for Baptists in Danbury, Connecticut.Source: The Wittenberg Door: Separation of church and state
The Connecticut state constitution endorsed Congregationalism. Although the Baptists were tolerated, they had serious concerns about discrimination; they were also concerned that the state government would start interfering with the operation of the church. So, in 1801, the Danbury Baptist Association took a bold step and wrote to the newly elected President of the United States—Thomas Jefferson.Our Sentiments are uniformly on the side of Religious Liberty – That Religion is at all times and places a Matter between God and Individuals – That no man ought to suffer in Name, person or effects on account of his religious Opinions – That the legitimate Power of civil Government extends no further than to punish the man who works ill to his neighbour: But Sir our constitution of government is not specific. Our antient charter, together with the Laws made coincident therewith, were adopted as the Basis of our government at the time of our revolution; and such had been our laws & usages, & such still are; that Religion is considered as the first object of Legislation; & therefore what religious privileges we enjoy (as a minor part of the State) we enjoy as favors granted, and not as inalienable rights: and these favors we receive at the expense of such degrading acknowledgements, as are inconsistent with the rights of freemen. It is not to be wondered at therefore; if those who seek after power & gain under the pretence of government & Religion should reproach their fellow men – should reproach their chief Magistrate, as an enemy of religion Law & good order because he will not, dares not assume the prerogative of Jehovah and make Laws to govern the Kingdom of Christ.Thomas Jefferson agreed with the Baptists that it was inappropriate for the state to interfere with maters of conscience, faith, and worship.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, & 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 & 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.If we are to use the term “separation between Church & State,” we must do so honestly, keeping the original context in mind: Thomas Jefferson was writing to Baptists who were being persecuted by an officially Congregationalist state government. Thus, he was not calling for a wall that protected the government from the church, but the church from the government—an important point to remember when discussing this topic.