There are 35 of these inconvenient quotes at Addicting Information. Here are the first five:

1. “If I could conceive that the general government might ever be so administered as to render the liberty of conscience insecure, I beg you will be persuaded, that no one would be more zealous than myself to establish effectual barriers against the horrors of spiritual tyranny, and every species of religious persecution.”
~George Washington, letter to the United Baptist Chamber of Virginia, May 1789

2. “Of all the animosities which have existed among mankind, those which are caused by a difference of sentiments in religion appear to be the most inveterate and distressing, and ought to be deprecated. I was in hopes that the enlightened and liberal policy, which has marked the present age, would at least have reconciled Christians of every denomination so far that we should never again see the religious disputes carried to such a pitch as to endanger the peace of society.”
~George Washington, letter to Edward Newenham, October 20, 1792

3. “We have abundant reason to rejoice that in this Land the light of truth and reason has triumphed over the power of bigotry and superstition… In this enlightened Age and in this Land of equal liberty it is our boast, that a man’s religious tenets will not forfeit the protection of the Laws, nor deprive him of the right of attaining and holding the highest Offices that are known in the United States.”
~George Washington, letter to the members of the New Church in Baltimore, January 27, 1793

4. “The United States of America have exhibited, perhaps, the first example of governments erected on the simple principles of nature; and if men are now sufficiently enlightened to disabuse themselves of artifice, imposture, hypocrisy, and superstition, they will consider this event as an era in their history. Although the detail of the formation of the American governments is at present little known or regarded either in Europe or in America, it may hereafter become an object of curiosity. It will never be pretended that any persons employed in that service had interviews with the gods, or were in any degree under the influence of Heaven, more than those at work upon ships or houses, or laboring in merchandise or agriculture; it will forever be acknowledged that these governments were contrived merely by the use of reason and the senses.”
~John Adams, “A Defence of the Constitutions of Government of the United States of America” 1787-1788

5. “The Government of the United States of America is not in any sense founded on the Christian religion.”
~1797 Treaty of Tripoli signed by John Adams