Free Thinker
The term free thinker is an artifact of modern thought, and is prototypically defined (at least in precursor form) by the thought of Rene Descartes, who believed that everything should be questioned, even belief in God, and should only be accepted on the basis of logic and reason. Descartes, rather conveniently, was able to invent all sorts of reasons to justify his Christianity. Others, of a more skeptical bent, who followed him, such as Voltaire and Nietzsche, found such reasons insufficient, and preferred to take free thought to a new level of materialism.
Although the pattern of increasing skepticism has continued to flourish, and even innovate (e.g. in the doctrine of the hermeneutic of suspicion) the notion of free thought has actually fallen into some disrepute along with the growth of a public philosophy described, albeit cynically, as political correctness. While this natural antagonism may be denied by some, it's too obvious even for many post-modern pundits to deny.