This article is quite wrongheaded. I can only dip into the problems with it, but I think it's worth addressing some of them, however briefly. (Here's hoping I close all my tags properly).

1.

The following paragraph is anachronistic in several different ways: "It was there [in Geneva] that his careful articulation of Christian theology [...] modeled many of the principles of liberty later embraced by our own Founders, including anti-statism, the belief in transcendent principles of law as the foundation of an ethical legal system, free market economics, decentralized authority, an educated citizenry as a safeguard against tyranny, and republican representative government which was accountable to the people and a higher law."

This is about as historically accurate as William Wallace's scream of "Freedom!" in Braveheart.

First, there was no such thing as the modern "state" in 1550, so there was no such thing as "anti-statism." A "state" was either the community itself, as in a republic, or the authority of a monarch, as in "the prince's state"; there was no state in the sense of an institution with an identity separate from the people running it. (So to be "anti-state" would be, by definition, treason -- except nobody would know what you were talking about in the first place.) Next, the "transcendent principles of law" were known to the Greeks and Romans and, indeed, the Catholics; this idea was not a Calvinist innovation. Third, "free market economics" would not be invented, indeed, would not be a comprehensible concept for another 200 years. (It was a response to economic developments that would not happen for another 100 years.) Fourth, "decentralized authority" is virtually meaningless in this context; we're talking about a city-state where almost everything happened in city-wide councils or else in a handful of district churches. Fifth, "republican representative government" is a combination of two different ideas. Geneva's government was supposed to consist of the magistrates of God, not the representatives of the will of the people. The people were responsible for making sure the magistrates did their job, i.e., were godly rulers, but they were not the magistrates' bosses; God was. The idea of representative government was a separate development related to the growth of Parliament in England.

2.

The American Revolution was run less by New England Presbyterians and Congregationalists than by (nominal) Southern and New York Anglicans. That is true both of the political thought and of the war effort. (Here is a handy though imprecise guide to the political thought part.) And many of the Congregationalists and Presbyterians were of questionable orthodoxy. John Adams, for example, was a Congregationalist with strong -- even emphatic -- Unitarian tendencies, despite his fond memories of Calvinism.

The fact is, Americans in different regions of the country had wildly different ideas about government and society. What they shared was not Calvinism, or even Protestantism, but a combination of English constitutional and legal thought and classical republican ideology -- which came from the Roman world via Italy.

3.

It is true that King George supposedly called the American War a "Presbyterian rebellion." However, he (a) was not exactly noted for the accuracy of his knowledge about colonial affairs, and (b) presumably was trying to insult the rebels by using that phrase. To any Englishman hearing the expression "Presbyterian rebellion," the immediate image to come to mind would be the English Civil War of 130 years before, when Presbyterians and Congregationalists in Parliament put the king to death and then squabbled among themselves so much that their republican government became a dictatorship (and then reverted to monarchy, to almost everyone's relief). There is no reason to think that George III actually knew what he was talking about or meant the expression literally.

4.

The paragraph on Michael Servetus is deeply and outrageously misleading. Here is Calvin's own description of Michael Servetus's arrest and trial, in a letter of 20 August 1553:

We have now new business in hand with Servetus. He intended perhaps passing through this city [Geneva]; for it is not yet known with what design he came. But after he had been recognised, I thought that he should be detained. My friend Nicolas summoned him on a capital charge, offering himself as security according to the lex talionis. On the following day he adduced against him forty written charges. He at first sought to evade them. Accordingly we were summoned. He impudently reviled me, just as if he regarded me as obnoxious to him. I answered him as he deserved. At length the Senate pronounced all the charges proven. Nicolas was released from prison on the third day, having given up my brother as his surety; on the fourth day he was set free. Of the man's effrontery I will say nothing; but such was his madness that he did not hesitate to say that devils possessed divinity; yea, that many gods were in individual devils, inasmuch as deity had been substantially communicated to those, equally with wood and stone. I hope that sentence of death will at least be passed upon him; but I desire that the severity of the punishment may be mitigated.

As for that last part -- Calvin's claim that he desired that "the severity of the punishment may be mitigated" -- he clarified this in a letter of 26 October 1553: "We endeavoured to alter the mode of his death, but in vain. Why we did not succeed I defer for narration until I see you." (Calvin wanted Servetus killed by the sword rather than by fire.)

And Calvin's determination to use the law against Servetus was of long standing. Here is a letter from seven years earlier: "Servetus lately wrote to me, and coupled with his letter a long volume of his delirious fancies [...]. He takes it upon himself to come hither [to Geneva], if he is agreeable to me. But I am unwilling to pledge my word for his safety, for if he shall come, I shall never permit him to depart alive, provided my authority be of any avail."

5.

I do not have time or space to address the John Adams quotations properly. They are a very interesting case. Phillips sort of gets the quotations right (though he leaves off the end), but he uses them in what I think is a misleading way, all things considered. For the record, they come from Adams's Discourses on Davila, written as a rebuke to the French Revolution, which was a highly controversial book among members of the Founding generation.