Like many secret(ive) societies, the Free Masons were speculated upon in public. They were known for having secret rituals, so in christian europe, this naturally led to rampant speculation on blasphemy, satanism, and heresy. Within specific denominations, there are (allegedly) conflicts of belief that disqualify christians from being accepted both by the church and the free masons—most vocally, the Catholic Church has forbidden their members from joining masonic lodges because they believed it was a deist belief system under a varnish of Christianity. I would source this, but it's 5:15AM and wikipedia has a huge number of sources itself, as well as many quotes that speak for themselves: https://en.wikipedia.org/wiki/Opposition_to_Freemasonry_within_Christianity

Unlike many secret(ive) societies, the free masons have flourished over the centuries. As a large, visible, christian cult surrounding ritual, fraternity, and (if I may be so bold) enlightenment values as a whole, it's hardly a surprise that wild speculation has cropped up about what the free masons "could be" if they were to, you know, decide to conspire and do something. You can see this in other ancient organizations too: the conspiracy theories surrounding the catholic church are myriad; old and somewhat forgotten organizations are the perfect marvelous setting for tall tales.

To look at this from another perspective, Pynchon is a master at creating utterly fictional paranoid fantasies. The Crying of Lot 49 is a great example of how you might go from a historical narrative (the postal service provided by the house of Tassis/Thurn und Taxis) into a full-blown conspiracy theory. The recipe? A power (in this case, postal mail, allowing one to dupe another into a false view of reality) and a mystery (pre-modern, sparsely documented, pre-industrial-revolution europe).