Another innovation of the new university was that higher education should be separated from religious doctrine. [The university] had no divinity school, was established independently of any religious sect, and the Grounds [campus] were planned and centered around a library, rather than a church, distinguishing it from peer universities still functioning primarily as seminaries for particular strain of Protestantism or another. Jefferson opined to philosopher Thomas Cooper that "a professorship of theology should have no place in our institution," and never has there been one.
Jefferson's insistence that the University of Virginia should be completely free of any religious connection did distinguish it from most institutions of higher education in America in the 18th and early 19th century centuries. As Rodney Stark informs us, "...prior to the [American] Revolution, ten institutions of higher learning had already begun operating in the American colonies (compared with two in England). Of these, only the University of Pennsylvania, instituted by Benjamin Franklin to train businessmen, was not affiliated with a denomination" (The Victory of Reason: H0w Christianity Led to Freedom, Capitalism, and Western Success, p. 227).
The irony for me is that by seeking to disconnect higher education from religious belief, Jefferson was, in effect, cutting off his university from its historical roots. The fact is that higher education as we think of it has its origins in the universities of medieval Europe. These universities owed their existence to the efforts of the Catholic Church to create an educated clergy. However, like many figures of the Enlightenment, Jefferson had a rather negative view of the Middle Ages and the religious beliefs that dominated that era, as evidenced by his reference to "monkish ignorance and superstition" in a well-known letter written just a few days before his death. It seems unlikely that Jefferson would have ever acknowledged the historical debt he owed to the medieval Church, without which he would not have possessed the very concept of the university. Still, to be fair, in this he was very much a child of his age--during which the characterization of the medieval period as the "Dark Ages" began to take hold. Only in more recent years have we began to realize that the "Dark Ages" are something of a myth.
Image of the Rotunda at the University of Virginia from Wikimedia Commons