According to Wikipedia:
"The actual term, "separation of church and state", does not appear in the Constitution, but rather derives from a letter written by Thomas Jefferson to a group identifying themselves as the Danbury Baptists."
http://en.wikipedia.org/wiki/Separation_of_church_and_state
Before him, a Renaissance Italian cleric, who died about the year Williams was born, Fausto Sozinni, better known as Faustus Socinus (1539-1604).
"When they [the Church] have opened a gap in the hedge or wall of separation between the garden of the church and the wilderness of the world, God hath ever broke down the wall itself, removed the Candlestick, etc., and made His Garden a wilderness as it is this day. And that therefore if He will ever please to restore His garden and Paradise again, it must of necessity be walled in peculiarly unto Himself from the world, and all that be saved out of the world are to be transplanted out of the wilderness of the World." -- Roger Williams 1603 - 1683