Question: Who was the first person to be referred to as a free-thinker?
Answer: John Toland (1670 - 1722)
The term free-thinker was coined by John Locke in reference to Toland, author of Christianity Not Mysterious.1 Toland felt that by applying Locke's epistemology to the Bible one could use reason to resolve any mystery or contradiction contained within. The book was burned in Ireland in 1696.
Toland is also notable for being credited with himself coining the term pantheist in 1705.
1. David Berman, "Disclaimers as Offence Mechanism in Charles Blount and John Toland," in Atheism, ed Hunter and Wootton, 269 - reference taken from Doubt: A history by Jennifer Michael Hectht, pg 335