Here is the relevant passage from Barton's book:
However, in that same letter of congratulations, the Baptists also expressed to Jefferson their grave concern over the entire concept of the First Amendment:
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, [and] that the legitimate power of civil government extends no further than to punish the man who works ill to his neighbor. But sir, our constitution of government is not specific...[T]herefore what religious privileges we enjoy (as a minor part of the State] we enjoy as favors granted, and not as inalienable rights.
The inclusion of Constitutional protection for the "free exercise of religion" suggested to the Danbury Baptists that the right was government-given (thus alienable) rather than God-given (hence inalienable), and that therefore the government might someday attempt to regulate religious expression. This was a possibility to which they strenuously objected--unless someone's religious practice caused him, as they explained, to "work ill to his neighbor" (pp. 43-44)
As is the case with his 1992 explanation of the Danbury letter, this argument is completely contrary to the facts. The Danbury Baptists were concerned with religious discrimination in the state of Connecticut; their letter to Jefferson does not reference the First Amendment or the federal Constitution in any way. Moreover, Barton knows the letter does not refer to the First Amendment; the ellipses in his quotation from the letter, above, omit exactly those words that would indicate to the reader that the constitution referenced here is the Connecticut state Constitution, and not the federal Constitution. Here is the section of the letter Barton quotes, with the omitted parts restored in italics:
Clearly, the constitution described here is the constitution of the state of Connecticut. Unlike the Connecticut constitution, the federal Constitution was not "ancient," was not adopted at the time of the revolution, didn't allow religion to be "the first object of legislation," did not subject Baptists (or any other denomination) to "degrading acknowledgments" as a condition of receiving religious privileges, and contained procedural safeguards that prevented government from assuming religious powers (the First and Tenth Amendments). Barton omits the italicized words knowing full well that if he included them in his quotation many readers would recognize that something is amiss with his account of the Baptists' letter.
Why does Barton argue that the Danbury Baptists wrote to Jefferson out of a concern about the potential misinterpretation of the First Amendment? Briefly, the argument serves as a foil for his belief that the First Amendment prohibits only preferential establishments of religion. Barton's argument is that the Danbury Baptists were concerned that, if the national government was allowed to limit religious expression, it would do so preferentially, thereby creating a preferential establishment of religion. Accordingly, Barton reads Jefferson's reply to the letter is nothing more than an endorsement of non-preferentialism:
Jefferson committed himself as President to pursuing what he believed to be the purpose of the First Amendment: not allowing the Episcopalians, Congregationalists, or any other denomination to achieve the "establishment of a particular form of Christianity."
Since this was Jefferson's view, in his short and polite reply to the Danbury Baptists on January 1, 1802, he assured them that they need not fear; the free exercise of religion would never be interfered with by the government (p. 45).
Once again, Barton's argument is at variance with the facts. The Baptists' concern was not about free exercise; it was about Connecticut's religious establishment, which taxed Baptists for the maintenance of Congregationalist churches unless they submitted to the "degrading" practice of obtaining exemption certificates which routed their tax money to their own congregations (see Derek Davis, "What Jefferson's Metaphor Really Means," Liberty, January/February, 1997, pp. 12-18). Baptists were free to worship in the state of Connecticut; their concerns were with establishment and its attendent effects. Additionally, Jefferson's reply to the Baptists is not specific to the issue of free exercise. On the contrary, the only mention of free exercise in the Danbury letter is in conjunction with the establishment clause, which together are held to erect the "wall of separation between church and state." Finally, if Barton is correct that Jefferson believed that the effect of the First Amendment is to prohibit government from "limit[ing], restrict[ing], regulat[ing], or interfer[ing] with public religious practices," then the Amendment prohibits all religious laws, not just preferential ones. Barton's evidence, in other words, even if it were true, would not lead to the conclusion he wants to reach.
Barton's 1996 account of the Baptists' letter is simply the latest in his long line of attempts to minimize the significance of Jefferson's "wall of separation" metaphor (his other attempts are examined here and here). It's a sad commentary on the state of accommodationist scholarship that one of the leading spokesmen for that cause is so willing to play fast and loose with the facts. Barton's mistakes are not of the sort that one can ascribe to honest scholarship. They are the product of a mind that is either incapable of seeing the truth, or presenting the truth with integrity.