It seems to me that masonic lodges arose as a way for the Third Estate, which was unrepresented in the
ancien régime, to organize for political influence. An increasingly educated and affluent society wanted greater freedom and self-determination. In the American colonies, this could be achieved with comparative ease, because it was a "new world". In "old world" Europe, the
ancien régime was much more firmly entrenched, and the effort to change it became correspondingly radicalized. Reactionary forces opposing the Masons supported the monarchy and the established church. Among those who get hysterical about the Masons today are those who are literal monarchists who oppose the disestablishment of the Catholic church.
Bottom line -- again, in my opinion -- it is really about power and money, not about religious belief.