How many of the founding fathers were christian/atheist?

The majority of the 100 plus founders were Christians, as were virtually all Europeans at that time. Of the Christian founders, most were very progressive in their views and were among the staunchest proponents of separation of Church and State. Some founders, including many of the most prominent, are known to have been Deists as well. Thomas Paine is of course the best example of an American Deist, but Benjamin Franklin also declared himself a Deist and Thomas Jefferson also wrote his own version of the Bible in which he took out all of the supernatural events of the New Testament. Benjamin Franklin is the only founder to have signed all three of the founding documents: the Declaration of Independence, The Treaty of Paris, and The Constitution. While Jefferson declared himself a "true Christian" (to Jefferson most priests and evangelicals were not "true Christians"), he also later declared himself an Epicurean. Epicures was a Greek materialist philosopher.

In a letter to William Short Jefferson proclaimed that, "[t]he immaculate conception of Jesus, his deification, the creation of the world by him, his miraculous powers, his resurrection and visible ascension, his corporeal presence in the Eucharist, the Trinity; original sin, atonement, regeneration, election, orders of Hierarchy, etc., [were all] invented by ultra-Christian sects, unauthorized by a single word ever uttered by him."

He followed  up that letter with another stating that, "[i]t is not to be understood that I am with him (Jesus Christ) in all his doctrines. I am a Materialist; he takes the side of Spiritualism; he preaches the efficacy of repentance toward forgiveness of sin; I require a counterpoise of good works to redeem it..."

It is certainly true that there were a great many highly Christian groups in early America, however it was in fact these very people that some of the founders were at odds with, as President Madison made clear in the quote above, calling those looking to retain a role of religion in government of "the old error."  He noted that there were such people in America, however these were not the people who founded America and established it as the most progressive country in the world at the time.

Furthermore, in 1797, in an attempt to establish peaceful relations with Muslims off the Northern Coast of Africa (an attempt that failed and led to the Barbary Wars), the Treaty of Tripoli was ratified by the Senate. Article 11 of the treaty states:

As the Government of the United States of America is not, in any sense, founded on the Christian religion; as it has in itself no character of enmity against the laws, religion, or tranquillity, of Musselmen; and as the said States never have entered into any war or act of hostility against any Mehomitan nation, it is declared by the parties that no pretext arising from religious opinions shall ever produce an interruption of the harmony existing between the two countries.

That is as plain as the issue of the government of America being founded on Christianity can be stated. This treaty was written during the end of Washington's presidency and signed by John Adams, with the above statement included, once he became president.

So as we see above, the religious faith of the founding fathers is irrelevant.  What truly matters is that they were secularists.  They were afraid of a state run church, both for the sake of the church and their personal beliefs.