Like most intelligent men, he did not consider the scriptures to be the direct word of God. He believed in God, of course. As a printer, he knew about printing errors. As a writer, he knew how a writer could slant something one way or another. As someone who spoke several languages, he knew about translation errors. As a member of the Constitutional Convention, he knew how committees could screw things up. He also knew that committees had had their hands on the Bible at least twice in its history. I know of three times.
When the Old Testament was first written down during the Babylonian Captivity
When the Catholic Church decided what would and what would not be included in the Bible (400s AD)
When the King James version was created.
Benjamin Franklin would have known about the last two.