Paul Thomas Anderson confirms The Master is based on L. Ron Hubbard, in case you still didn't get that

Ever since The Master was first announced, Paul Thomas Anderson has been pointedly demure about whether the film is explicitly about Scientology, simply because it concerns the founder of a 20th-century religion steeped in principles of self-determinism who comes to be accused of running a cult, as his followers resort to aggressive tactics to defend him. Also a topic which Anderson hasn't felt like discussing: whether he screened The Master for his Magnolia star and friend Tom Cruise, and whether this then resulted in Tom Cruise quietly seething for 20 minutes. "Why are you so fascinated by my Forbidden Closet Of Scientology Mystery?" Anderson has basically been saying—until now, at the Venice Film Festival, where Anderson finally admitted that, yes, Philip Seymour Hoffman's character is inspired by Scientology founder L. Ron Hubbard, presumably shortly after confirming that There Will Be Blood is about oil.

Nevertheless, Anderson was quick to add that The Master should not be seen as some sort of exposé of the movement, seeing as it really only reflects Anderson's knowledge about Scientology's origins, it's meant to be a drama about the relationship between Hoffman's character and the tormented alcoholic played by Joaquin Phoenix, and Anderson would like to not get sued, please. And speaking of uneasy relationships, Anderson also confirmed that he had screened the film for Cruise—though he didn't offer much beyond that, saying only, "We are still friends. I showed him the film, and the rest is between us." So, definitely nothing else to wonder about there.