Well they had slaves didn't they?
If you think free thinkers weren't persecuted by christians in this country I should point you to the history of Salem.
Most of the founders were secularists even though most were Christians. It's possible to be both.
Thomas Pain himself was at the very least an agnostic.
Thomas Jefferson wrote his own heretical version of the bible.
"The hocus-pocus phantasm of a God like another Cerberus, with one body and three heads, had its birth and growth in the blood of thousands and thousands of martyrs." --Jefferson
"If we look back into history for the character of the present sects in Christianity, we shall find few that have not in their turns been persecutors, and complainers of persecution. The primitive Christians thought persecution extremely wrong in the Pagans, but practiced it on one another. The first Protestants of the Church of England blamed persecution in the Romish Church, but practiced it upon the Puritans. They found it wrong in Bishops, but fell into the practice themselves both here (England) and in New England." --Franklin
"What influence, in fact, have ecclesiastical establishments had on society? In some instances they have been seen to erect a spiritual tyranny on the ruins of the civil authority; on many instances they have been seen upholding the thrones of political tyranny; in no instance have they been the guardians of the liberties of the people. Rulers who wish to subvert the public liberty may have found an established clergy convenient auxiliaries. A just government, instituted to secure and perpetuate it, needs them not." --Madison
"The divinity of Jesus is made a convenient cover for absurdity. Nowhere in the Gospels do we find a precept for Creeds, Confessions, Oaths, Doctrines, and whole cartloads of other foolish trumpery that we find in Christianity." --Adams
"Whenever we read the obscene stories, the voluptuous debaucheries, the cruel and torturous executions, the unrelenting vindictiveness, with which more than half of the Bible is filled, it would be more consistent that we call it the word of a demon than the word of God. It is a history of wickedness that has served to corrupt and brutalize mankind." --Paine