In the bio of Franklin I'm reading, there's a whole chapter on his religion.
He was raised a Puritan in Boston, but rejected his parents' religion early on in his childhood. The contradictions between a benevolent all-knowing God and the random catastrophes that strike good people were just too much for him to reconcile.
He was accused of being an atheist, but he defined himself as a deist. He believed in one all-powerful supreme being that created the world, but he did not believe the god was concerned with man's day-to-day life. Nor did he imagine this god cared about being worshipped. So he was not a church-goer.
His was a god not of daily life, but only of first causes.
If one is going to imagine gods, this seems like the most intelligent choice. First causes are mysterious, and science really does not much better a job at them than religion. How did the universe form, and why? What was before? Where does it end? How did the first life form? These are deep, deep questions without good scientific answers.
Knowing that the answers are unknowable puts religious explanations ("just so" stories) about on par with explanations that say, "something happened here that we can't explain, that hasn't happened again, and violates all the rules we know."
Such a god -- a distant unknowable god having no intersection with the world -- is so close to a non-god that an atheistic scientific world view is essentially indistinguishable. Except the atheist allows that maybe, someday, further understanding might be possible.
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