It came from the fact that Jefferson, Paine, and Franklin were not Christians and i wouldnt classify it soley as a myth since there is some truth in it.
There is absolutely no truth in "the majority of our Founders weren't Christians".
And...
Thomas Jefferson
SIGNER OF THE DECLARATION OF INDEPENDENCE; DIPLOMAT; GOVERNOR OF VIRGINIA; SECRETARY OF STATE; THIRD PRESIDENT OF THE UNITED STATES
The doctrines of Jesus are simple, and tend all to the happiness of man.64
The practice of morality being necessary for the well being of society, He [God] has taken care to impress its precepts so indelibly on our hearts that they shall not be effaced by the subtleties of our brain. We all agree in the obligation of the moral principles of Jesus and nowhere will they be found delivered in greater purity than in His discourses.65
I am a Christian in the only sense in which He wished anyone to be: sincerely attached to His doctrines in preference to all others.66
I am a real Christian – that is to say, a disciple of the doctrines of Jesus Christ.67
Benjamin Franklin
SIGNER OF THE DECLARATION; DIPLOMAT; PRINTER; SCIENTIST; SIGNER OF THE CONSTITUTION; GOVERNOR OF PENNSYLVANIA
As to Jesus of Nazareth, my opinion of whom you particularly desire, I think the system of morals and His religion as He left them to us, the best the world ever saw or is likely to see.30
The body of Benjamin Franklin, printer, like the cover of an old book, its contents torn out and stripped of its lettering and guilding, lies here, food for worms. Yet the work itself shall not be lost; for it will, as he believed, appear once more in a new and more beatiful edition, corrected and amended by the Author.31 (FRANKLIN’S EULOGY THAT HE WROTE FOR HIMSELF)
Thomas Paine, I believe, was actually an atheist.
I don't know any other founder that wasn't deeply religious.