I have followed this debate with great interest. On the one hand, as some rightly declare, the central government was much weaker at our nation's founding than at present. To be sure there have been some guilty of projecting their biases on the past with regards to Federal power and the issue of religion. Conversely, I would argue that many on this list also project their preferred understanding of the past in a kind of presentism that also fails to capture an understanding of our nation at birth.
Indeed, we need to be mindful that in New England only 84 years before the Declaration of Independence was penned by Jefferson, religious zealots still busied themselves by burning witches at the stake. Indeed, the jihadist beheaders of American journalist Daniel Pearl might have felt quite comfortable in that America rather than our present United States.
As we know our original founding document, the Articles of Confederation, restricted Federal power by design. The great fear of many founders, especially the Anti-Federalists, was the hijacking of the republic by the military and/or by a charismatic leader that would impose his/their will (which could include a religion) on the people.
It is also clear that many (not all) founders were influenced by the Enlightenment and Deism. Among those were Jefferson. Jefferson has endless quotes pronouncing his relegation of religion to the states and as many to the individual. For Jefferson, the question of individual rights was best protected by local government, and the more local the better. That said, the Anti-Federalists were keen to ensure that neither states nor the Federal Government would impose state religions and would protect individual liberties.
Indeed, writing on the topic of religious tolerance and protection of such rights to “Hindoo (sic) and Infidel of every denomination”:Where the preamble (to the Virginia Constitution) declares, that coercion is a departure from the plan of the holy author of our religion, an amendment was proposed by inserting "Jesus Christ," so that it would read "A departure from the plan of Jesus Christ, the holy author of our religion;" the insertion was rejected by the great majority, in proof that they meant to comprehend, within the mantle of its protection, the Jew and the Gentile, the Christian and Mohammedan, the Hindoo and Infidel of every denomination.
In conclusion, some general points:
1) ironically, it was the more (not total, but more) secularist Anti-Federalists who were the chief advocate of States’ Rights. Whereas the more religious, Federalists, were for increased central control in government generally. This is, of course, the opposite of today, with today’s religiously minded projecting their present view of states’ rights onto the past regarding States’ Rights.
2) the state churches referenced, such as in Mass. (entrenched bureaucracies with powers to tax) were all gone by the 1830s. The Federal government was fairly weak at its inception, but what is interesting to note is not the persistence of state religion, but how with a few short decades of the Constitution’s pronouncements against state religion, that even in the land of the Salem Witch Trials, state churches were gone. Rather than being in the ascendant, state churches were on the way out.
3) Jefferson support for all beliefs reflected his libertarianism on such matters. He himself worked to secularize Christianity through the publication of his own Bible that reduced it to an enlightenment book of moral philosophy that cleansed it of all supernatural acts. No mere flip comment, it represents a serious, sustained document of his personal philosophy, and he makes it very clear where he stands.
4) Lastly, regarding Jefferson as a Christian, the Federalists in the 1800 election most certainly did not think him one, and made Jefferson’s “deism,” as the Federalists saw it, their central attack in that campaign. Of course, some of this was political opportunism. The Federalists lost this election, which provides further evidence of weakening religion among elites, who at this time constituted most voters.