Whoever told you that the Founding Fathers were not Christian was gravely mistaken. Many (but by no means all) of the Founders subscribed to a philosophical approach to Christianity known as Deism. Deism posits that there is an all-powerful creator who was responsible for forming the world, but that this creator no longer takes an active role in the world. It arose as a response to a dissatisfaction with organized religion among the educated classes in the United States and Western Europe in the eighteenth century. Thomas Jefferson was rather famously a Deist, as was Thomas Paine, writer of famous Revolutionary pamphlets like Common Sense. Paine, in fact, eventually professed a level of atheism that made his former allies uncomfortable.

However, that is not to say that the broader population of White European settlers startling in the sixteenth century were not Christian. All of those who founded colonies were adherents of various forms of Protestant Christianity, with the notable exception of Maryland, which was founded as a Catholic haven. The most famous British-American colonists, the Pilgrims and Puritans of what is today Massachusetts, in fact adhered to a rather severe movement in Christianity called--you guessed it--Puritanism. But even in colonies like Virginia, where religion was less central to everyday life, the colonists and their backers in England were Anglicans. One of the justifications for British colonizations in fact came to be called the Black Legend, the idea that barbarous Spanish Catholics had perpetrated horrible crimes in their South American colonies, thus justifying English attacks on Spanish treasure ships and attempts to wrest colonies away from them.

Anyway, the Founders explicitly sought to limit the influence of Christianity and other religions on our governmental structure. They were to a man, however, raised in a Christian environment, even if some proportion of them were Deists or otherwise unaligned with formal religion. Harvard University, the first university founded in what is now the United States, was founded explicitly to train future Congregationalist (the name for the established Puritan church) ministers. This gave way to Unitarianism in the nineteenth century. Harvard's history as a fully secular institution is really fairly short.

For a good look at the status of American Christianity around the time of the Revolution, I like Nathan O. Hatch's The Democratization of American Christianity.