John Leland, a Baptist preacher, “emerged a leader among the Commonwealth’s Baptists. He was instrumental in allying the Baptists with Jefferson and Madison in the bitter Virginia struggle to disestablish the Anglican Church and to secure freedom for religious dissenters.” According to L.H. Butterfield, Leland “was as courageous and resourceful a champion of the rights of conscience as America has produced.”
Leland, who allied with the Baptists, supported Jefferson because of his commitment to “the rights of conscience.” This did not refer to separating religious beliefs from politics, but rather allowed one to believe according to his own conscience without government interference. For example, Leland celebrated Jefferson’s election from his pulpit. By conscience, they referred to the first table of the Ten Commandments as Roger Williams did. Conscience refers to opinions so referred to by both Jefferson and the Danbury Baptists in their correspondence.
Generally, Baptists, dissenters, and Republicans were supporters of Jeffersonian Republicanism because of the emphasis of religious freedom whereas the New England Congregationalists, establishment clergy, and Federalists were not because of their belief in a stronger relationship between state and church. In Jefferson’s letter to the Danbury Baptists he said, “Believing with you that religion is a matter which lies solely between man and his God, that he owes account to none other for his faith or worship, that the legislative 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.” (italics added)
Note that the wall protected the reality that a person’s faith and worship was between God and him alone. The wall protected man from having to give an account for his faith to the federal government. Baptists had fought alongside Jefferson for the disestablishment of the established church in Virginia. The First Amendment phrase “Congress shall make no law respecting an establishment of religion” was in that historical context.
That this is Jefferson’s emphasis is even clearer in his second inaugural address when he said, “In matters of religion I have considered that its free exercise is placed by the Constitution independent of the power of the General Government. I have therefore undertaken on no occasion to prescribe the religious exercises suited to it, but have left them, as the Constitution found them, under the direction and discipline of the church or state authorities acknowledged by the several religious societies.“ (italics added)
Constitutional law authority Edward S. Corwin says of Jefferson’s statement, “In short, the principal importance of the amendment lay in separation which it effected between the jurisdiction of state and nation regarding religion, rather than on its bearing on the question of the separation of church and state.” Similarly, Daniel Dreisbach, Professor of Law, American University comments, “Jefferson’s wall, strictly speaking, was a metaphoric construction of the First Amendment, which governed relations between religion and the national government. His wall, therefore, did not specifically address relations between religion and state authorities.”
Dreisbach further notes, “Jefferson’s wall, like the First Amendment, affirmed the policy of federalism. This policy emphasized that all governmental authority over religious matters was allocated to the states. The metaphor’s principal function was to delineate the legitimate jurisdictions of state and nation on religious issues. Insofar as Jefferson’s wall, like the First Amendment, was primarily jurisdictional (or structural) in nature, it offered little in the way of a substantive right or universal principle of religious liberty.”
Further confirming Jefferson’s jurisdictional understanding is the fact that he sent his letter to the Danbury Baptists on 1/1/1802, which was the same day that Baptist Pastor John Leland brought him the Cheshire cheese as a betokening of celebration of his election as president. Additionally, Leland accepted an invitation to preach in the House of Representatives 1/3/1802, which Jefferson attended, just two days after Jefferson used wall of separation in his letter.  Jefferson asked for prayer in his second inaugural address. In addition, “so far as the extant evidence indicates, he never again used the wall metaphor.” Jefferson concluded the Danbury letter with prayer as an official presidential act. “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 and esteem.”
Based upon Jefferson’s understanding of the First Amendment, he was disinclined to make public religious proclamations like his predecessors (although congruent with his view of state rights, he did do so as governor of Virginia), but he was not so disinclined to use religious language that was virtually indistinguishable from previous religious proclamations.
 Daniel L. Dreisbach, Thomas Jefferson and the Wall of Separation between Church and State, (New York: New York University Press, 2002), 13.
 L.H. Butterfield, “Elder John Leland, Jeffersonian Itinerant,” Proceedings of the American Antiquarian Society 62 (1952): 157, as quoted by Dreisbach, Thomas Jefferson, 13.
 Herbert M. Morais, “Life and Words of Elder John Leland” (M.A. thesis, Columbia University, 1928), 44-50 as quoted by Dreisbach, Thomas Jefferson, 13.
 Dreisbach, Thomas Jefferson, 10.
 Church and State in Your Community (Philadelphia: WestMinister Press, 1964), 22.
 Dreisbach, Thomas Jefferson, 51-53. New England Baptists did not support Jefferson’s use of wall of separation or his deism. No New England Baptists ever used the phrase.
 Rus Walton ed., Biblical Principles concerning issues of importance to Godly Christians, (Plymouth, Mass.: Plymouth Rock Foundation, 1984) 226.
 Walton, Biblical Principles, 227.
 Dreisbach, Thomas Jefferson, 50.
 Dreisbach, Thomas Jefferson, 69.
 Dreisbach, Thomas Jefferson, 17.
 Dreisbach, Thomas Jefferson, 21.
 Dreisbach, Thomas Jefferson, 174, note 11.
 Dreisbach, Thomas Jefferson, 54.
 Thomas Jefferson, The Writings of Thomas Jefferson, Albert E. Bergh, ed. (Washington, D. C.: The Thomas Jefferson Memorial Association of the United States, 1904), Vol. XVI, 281-282.