Bishop Meade, a founding era figure, testified on the deplorable conditions of orthodoxy in 18th Century Virginia, especially at the College of William and Mary.

The intimacy produced between infidel France and our own country, by the union of our arms against the common foe, was most baneful in its influence with our citizens generally, and on none more than those of Virginia. The grain of mustard-seed which was planted at Williamsburg, about the middle of the century, had taken root there and sprung up and spread its branches over the whole State, --the stock still enlarging and strengthening itself there, and the roots shooting deeper into the soil. At the end of the century the College of William and Mary was regarded as the hotbed of infidelity and of the wild politics of France. Strong as the Virginia feeling was in favour of the Alma Mater of their parents, the Northern Colleges were filled with the sons of Virginia's best men.

Likewise Timothy Dwight had problems with "infidelity" at Yale. As this book notes:

We are now entering upon a very interesting period in the life of Dr. Dwight. Owing to a variety of causes which it is not necessary to enumerate, the state of Yale College at the time of his accession to the office of President, was in many respects unhappy. Destitute in a great degree of public or private patronage, its numbers were reduced, its discipline was relaxed, a looseness of moral and religious sentiment had become fashionable, and its reputation had been for some time on the decline through the community. One of the greatest evils under which it suffered, was an extensive prevalence of infidelity among the students. This pernicious spirit had been derived from the circumstances of the country at the close of the preceding war. As was natural, it found easy access to the minds of a collection of youths, who were fascinated with ideas of mental as well as political independence, and who were easily induced to shake off what they considered the shackles of habit and superstition. The degree to which it prevailed may be conjectured from the following fact. A considerable proportion of the class which he first taught, had assumed the names of the principal English and French infidels, and were more familiarly known by them than by their own. Under circumstances like these, he entered upon the duties of his office as PRESIDENT OF YALE COLLEGE.

Or as a more modern source (and one sympathetic to Dwight's creed) puts it:

When Dwight arrived at Yale, the moral and scholarly atmosphere of the school was, to say the least, in a valley. Membership in the college church hovered near, well, near zero. Most undergraduates avowed themselves skeptics. One of the students of that day later wrote, ``intemperance, profanity, and gambling were common; yea, and also licentiousness.'' Some of the students had taken to calling each other not by their given names, but rather by the names of Voltaire, D'Alembert, Diderot, and of other French and English infidels. The campus supported not one but two societies dedicated to the reading and distribution of literature by deist Tom Paine. One might think that in such an atmosphere of "reason" and of worship of the exalted human nature order and self-discipline might have also been prominent on campus. As with the French revolution, however, such talk in its practical application degenerated into pleasure seeking, and gratification of the true nature of humanity. Once, near the end of his term, when the previous president of Yale had brought a visitor to the chapel for an assembly, he, being late, found the students yelling, whooping, carousing, and generally out of control. The president forced his way to the podium and wore himself out shouting and pounding on the stage with his cane until the cane splintered. It was some time before order was restored.

One reason Yale may have been so sympathetic to infidelity prior to Dwight's Presidency was the previous President (Dwight became President in 1795) was Ezra Stiles. Now, Stiles too was an orthodox Christian. He was also a patriot preacher (preached pro-revolutionary sermons from the pulpit), a fervent Whig, and himself imbibed in enlightenment dogma. He was precisely the type of "Christian" susceptible to the theistic rationalism that captured the minds of Adams, Franklin, Jefferson, and many others, though he never (as far as I know) became one. Stiles did, however, support the French Revolution.

Dwight, because of his talent, apparently succeeded in quelling the infidel temptation at Yale. But at Harvard, infidelity triumphed. George Whitfield, of Great Awakening fame, observed, in 1740, how infidelity infiltrated Harvard. As Samuel Morison put it in a study of Harvard:

Harvard College and the Congregational Church were broadening down from primitive Calvinism to eighteenth-century theism or Unitarianism. This peaceful process was rudely interrupted by an evangelical revival known as the Great Awakening. The preliminary rumblings of that movement in the Connecticut Valley did not disturb Cambridge; but in September, 1740, the whirlwind revivalist George Whitefield arrived in Boston, addressed fifteen thousand people on Boston Common, and on the twenty-fourth preached to students and townspeople in Cambridge meetinghouse. Harvard men were divided in opinion as to the wisdom and value of this first of modern revivals.... Conservatives who deplored the liberal tendencies of the age were delighted at the straight hell-and damnation Calvinism that Whitefield preached.... Whitefield was entertained by President Holyoke, and listened to with eager attention by the students; but he found little to praise at Harvard, where...the state of "piety and true godliness" was not much better than at Oxford and Cambridge. "Tutors neglect to pray with, and examine the hearts of, their pupils," who read "bad books" such as the works of Tillotson and Clarke. Whitefield observed that "Many Scholars appeared to be in great concern as to their souls."24

As Josiah Quincy recounts the incident:

The controversy with Whitefield was the last of a tic theological character in which the governors of the New England College directly engaged. As doctrinal disputes grew more intense and critical, they stood aloof, realizing the wisdom of conducting the seminary exclusively as a literary, rather than as a theological institution. At this period the high Calvinistic doctrines prevailed throughout New England, but chiefly predominated in the interior of Massachusetts, and in the Colony of Connecticut. In Boston and its vicinity, and along the seaboard of Massachusetts, clergymen of great talent and religious zeal openly avowed doctrines which were variously denounced by the Calvinistic party as Arminianism, Arianism, Pelagianism, Socinianism, and Deism. The most eminent of these clergymen were alumni of Harvard, active friends and advocates of the institution, and in habits of intimacy and professional intercourse with its governors. Their religious views indeed received no public countenance from the College; but circumstances gave color for reports which were assiduously circulated throughout New England, that the influences of the institution were not unfavorable to the extension of such doctrines. The College became, in consequence, an object of severe scrutiny and some reproach, not the less severe from the fact that one or more members of the Corporation were among the most zealous of the Calvinistic sect. The attack made by Whitefield on the College was in coincidence with these reports.

These men, Harvard alum preaching "Arminianism, Arianism, Pelagianism, Socinianism, and Deism" from the pulpit, disproportionately were patriot Whig preachers arguing on behalf of Revolution -- notable among them, Jonathan Mayhew, Charles Chauncy, Simeon Howard, and Samuel West.  The orthodox failed to root out infidelity from Harvard.  In 1747, they unsuccessfully attempted to boycott unitarian Jonathan Mayhew's ordination.  And by 1805 Unitarian Henry Ware was elected to head Harvard's Divinity studies.  Starting with John Thornton Kirkland, "[f]rom 1810 until 1933 all of the presidents of Harvard University were Unitarians."

Many of the men studying in the founding era seminaries and preaching pro-revolutionary sermons from the pulpit, though they quoted the Bible, intermixed it with a-biblical enlightenment rationalism and elevated reason and natural theology over revelation.  Leading lights like Mayhew, Chauncy, West, Howard, and many others including America's key founding fathers, as theological unitarians and universalists arguably weren't "Christians" (at least not as evangelicals or Catholics understand the term).  Keep that in mind next time proponents of the Christian America thesis note the involvement of ministers or figures with "seminary" degrees who played key roles in America's founding.