Religious Tolerance in a Christian Nation?

The Virginia Statute for Religious Freedom was one of Thomas Jefferson's proudest achievements, so much so that his tombstone reads

HERE WAS BURIED
THOMAS JEFFERSON
AUTHOR OF THE
DECLARATION
OF AMERICAN INDEPENDENCE
OF THE
STATUTE OF VIRGINIA
FOR
RELIGIOUS FREEDOM
AND FATHER OF THE
UNIVERSITY OF VIRGINIA
BORN APRIL 2, 1743 O.S.
DIED JULY 4. 1826

Of the statute, Jefferson wrote [and is often quoted]:

The bill for establishing religious freedom, the principles of which had, to a certain degree, been enacted before, I had drawn in all the latitude of reason & right. It still met with opposition; but, with some mutilations in the preamble, it was finally passed; and a singular proposition proved that it's protection of opinion was meant to be universal. Where the preamble declares that coercion is a departure from the plan of the holy author of our religion, an amendment was proposed, by inserting the word "Jesus Christ," so that it should read "a departure from the plan of Jesus Christ, the holy author of our religion." The insertion was rejected by a great majority, in proof that they meant to comprehend, within the mantle of it's protection, the Jew and the Gentile, the Christian and Mahometan, the Hindoo, and infidel of every denomination.

It's indisputable that the Virginia scheme was more or less followed in the states, that all religions were protected. But let's look closely at where this freedom comes from.

"Jesus Christ" is explicitly not added, perhaps for the reason Jefferson gives, that all religions are protected. But that's the "plan" of "the Holy author of our religion," a phrase that remains in the text of the statute.

Where as Almighty God hath created the mind free; that all attempts to influence it by temporal punishments or burthens, or by civil incapacitations, tend only to beget habits of hypocrisy and meanness, and are a departure from the plan of the Holy author of our religion, who being Lord both of body and mind, yet chose not to propagate it by coercions on either, as it was in his Almighty power to do...

One might argue that Virginia's statute [the least explicitly religious of all the states] had some other "author" and "religion" in mind than Jesus or the God of the Bible. Jefferson is well-known for his personal skepticism about that stuff.

But Who is this Holy author, and of what religion?

For George Washington's Circular Letter to the States[1783] that announced his stepping down as the Continental Army's commander-in-chief [the revolution was won!], uses "divine author of our blessed religion" in the clear context of Jesus Christ.

"Charity, humility and pacific temper of mind, which were the Characteristics of the Divine Author of our blessed Religion..."

And although it's true that Washington probably didn't personally write it, this indicates what the common meaning of the phrase was, and Washington did sign it in his own hand.

And even in Massachusetts, which had an officially established church, we see the orthodox Calvinist Samuel Adams write as early as 1772 that religious tolerance, via John Locke himself, has become a feature of Christianity:

In regard to religion, mutual toleration in the different professions thereof is what all good and candid minds in all ages have ever practised, and, both by precept and example, inculcated on mankind. And it is now generally agreed among Christians that this spirit of toleration, in the fullest extent consistent with the being of civil society, is the chief characteristical mark of the Church. Insomuch that Mr. Locke has asserted and proved, beyond the possibility of contradiction on any solid ground, that such toleration ought to be extended to all whose doctrines are not subversive of society.

And so, if it be argued that America's religious tolerance was the product of a rising secularism, it can also be argued that the prevailing sentiment of the day was that religious freedom was demanded and guaranteed by Christianity itself.

Regardless of Jefferson's personal theological beliefs, he couldn't avoid using Christian arguments, and that's what got Christians to sign on the dotted line.