Jefferson's letter to Benjamin Rush shows that Jefferson was a non-preferentialist.

[Jefferson] believed, along with the other Founders, that the First Amendment had been enacted only to prevent the federal establishment of a national denomination--a fact he made clear in a letter to fellow-signer of the Declaration of Independence Benjamin Rush:

[T]he clause of the Constitution which, while it secured the freedom of the press, covered also the freedom of religion, had given to the clergy a very favorite hope of obtaining an establishment of a particular form of Christianity through the United States; and as every sect believes its own form the true one, ever one perhaps hoped for his own, but especially the Episcopalians and Congregationalists. The returning good sense of our country threatens abortion to their hopes and they believe that any portion of power confided to me will be exerted in opposition to their schemes. And they believe rightly (p. 45).

There is little to commend this argument. In particular, we note that Barton's conclusion is illogical; one cannot conclude from Jefferson's opposition to preferential establishment that he believed the effect of the First Amendment was limited to preferential establishment. This would be the same as arguing that, because Jefferson believed that the free speech clause prohibited the Sedition act of 1798, the free speech clause was limited to sedition! In fact, Jefferson indicated on numerous occasions that he believed the First Amendment was a total prohibition on the power of government to aid or hinder religion:

• I consider the government of the United States as interdicted by the Constitution from intermeddling in religious institutions, their doctrines, discipline, or exercises. This results not only from the provision that no law shall be made respecting the establishment or free exercise of religion, but from that also which reserves to the states the powers not delegated to the United States. Certainly, no power to prescribe any religious exercise or to assume authority in religious discipline has been delegated to the General Government. It must rest with the States, as far as it can be in any human authority (letter to Samuel Miller, Jan. 23, 1808).

• In matters of religion, I have considered that its free exercise is placed by the constitution independent of the power of the federal 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 of state or church authorities acknowledged by the several religious societies (Jefferson's Second Inaugural Address).

• In justice, too, to our excellent Constitution, it ought to be observed, that it has not placed our religious rights under the power of any public functionary. The power, therefore, was wanting, not less than the will, to injure these rights (Letter to the Society of the Methodist Episcopal Church at Pittsburg, Dec. 9, 1808).