The first Harvard president of note was Henry Dunster, a 30-year-old graduate of Cambridge University who arrived in Boston in 1640. He expected the new college to live up to the standards of England's two great universities, Oxford and Cambridge. A three-year course in the Liberal Arts, the Three Philosophies, and the Learned Tongues was instituted for the Bachelor's degree.
In 1650 President Dunster was able to obtain from the General Court, the colony's legislature, the Charter under which Harvard University still operates. The president and treasurer and five fellows were incorporated as the ruling body of the college. In later years they became known as the overseers. Samuel Eliot Morrison writes in Three Centuries of Harvard (p. 23):
A learned clergy was the immediate and pressing social need that Harvard was expected to supply; but the advancement of learning was the broad purpose of the College. Harvard students were reminded that the object of their literary and scientific studies was the greater knowledge of God; and that the acquisition of knowledge for its own sake, without "laying Christ in the bottome, as the only foundation" was futile and sinful.
Such was the basic philosophy of the College. There was always the fear among the colonists that without religious education, their children would become barbarous. Which is exactly what has happened today. Secular education without biblical religion is indeed creating an ignorant and barbarous youth.
By the 1690s, liberal, anti-Calvinist influences began to infiltrate the governing body of the college. And by 1701, Harvard's liberal tendencies had become so pronounced that a new orthodox college was founded at New Haven, Connecticut, which became Yale University. All the founders of Yale were Harvard graduates in the Connecticut Valley or on Long Island Sound.
On October 28, 1707, John Leverett became President of Harvard. This was the first time that a layman and a liberal was elected to an office hitherto held by an orthodox Puritan minister. Although Leverett instituted no changes in the curriculum, his liberal policies began to be reflected in student behavior. He wrote in his own diary in 1717 that the faculty was having trouble with "profane swearing," "riotous Actions," and "bringing Cards into the College." Many college clubs were formed by students, which encouraged questionable behavior.
By 1800, the liberal seed, first sown by Leverett, became the full-blown fruit of Unitarianism, which rejected the Trinity, rejected the divinity of Christ, and rejected all the tenets of Calvinism, along with centuries of even older orthodox Christian theology. The final battle that ended the ongoing war between the orthodox and Unitarians took place in 1805 when Reverend Henry Ware, a Unitarian minister, was elected Hollis Professor of Divinity. Morrison writes (p. 189): "Thus the theological department of New England's oldest university went Unitarian. Orthodox Calvinists of the true Puritan tradition now became open enemies to Harvard."
Actually, it was the other way around. It was the Unitarians who considered Calvinists to be their primary enemies, setting Harvard on a secular course that would become increasingly non-Christian. The distaste that Harvard liberals today show toward Christian fundamentalism is a continuation of their war against trinitarian orthodoxy. It should be noted that secular humanism is a direct outgrowth of Harvard's Unitarian philosophy.
Unitarianism is not a revealed religion. It is a social movement based on the notion that man is basically good and morally perfectible, and that all that is needed to achieve this moral and social utopia is a good secular education. And that is why the Unitarians became the major force in the public school movement.
It should also be noted that Unitarian liberalism is at the core of American political liberalism, for the chief practice of Unitarians was and still is social political activism based on the belief that government could solve all of our problems. And that's the liberal political philosophy that prevails today.