Let's begin with the definition of "Freethought": (At this point in time,) Wikipedia says:
"Freethought holds that individuals should neither accept nor reject ideas proposed as truth without recourse to knowledge and reason. Thus, freethinkers strive to build their beliefs on the basis of facts, scientific inquiry, and logical principles, independent of any factual/logical fallacies or intellectually-limiting effects of authority, cognitive bias, conventional wisdom, popular culture, prejudice, sectarianism, tradition, urban legend, and all other dogmatic or otherwise fallacious principles. As such, when applied to religion, the philosophy of freethought holds that, given presently-known facts, established scientific theories, and logical principles, there is insufficient evidence to support the existence of supernatural phenomena.
A line from "Clifford's Credo" by the 19th Century British mathematician and philosopher William Kingdon Clifford perhaps best describes the premise of freethought: "It is wrong always, everywhere, and for anyone, to believe anything upon insufficient evidence." (see evidentialism) Since many laws, doctrines, and popular beliefs are based on dogmas, freethinkers' opinions are often at odds with commonly held established views."
That kinda gets us there. Freethought requires evidence before belief. Freethinkers are not exactly anti-religion, but the philosophy often leaves them at odds with some religions, particularly those that use a very literal interpretation of their particular dogma.