Luther ultimately led to the subjection of the national churches to the state.
With a bit of help from people like Robespierre, Karl Marx and Henry VIII. The point is that Luther loosened the grip of the medieval church on the psyche of man and set it free to behave responsibly or otherwise so long, in Luther's view, he adhered to the Scriptures. Thomas Jefferson, at least in the Declaration of Independence, exercised that liberty of conscience responsibly even though he was a devoted censer of the Scriptures.
So Thomas Jefferson, a quintessential man of the Enlightenment, took part of Luther's freedom of conscience and rejected that part which tied him to the Scriptures, which he despised.