Yeah, it's a story of the beginning of a cult, so it's not going to make much sense. I get it. But they go beyond that to make it a really bad movie. The big problem is they put the plot focus on the mentally unstable character Freddie Quall, played by Joaquin Phoenix. The problem with Quall is he's not really disturbing (which could be fascinating, see Hannibal Lecter), but just disturbed. You can't make a movie surrounding a character like that! He's not "compelling", he's not "interesting", he's just sad. The writers made a terrible blunder by making this guy TOO disturbed, so disturbed you feel like you're staring at a homeless guy, trying to figure out when he's going to eat his own feces. That makes YOU the creepy one!
This, and other choices by the filmmakers, makes "The Master" a sloppy, unwatchable mess. Besides focusing too much on Quall's lunacy, it skips & jumps around and just when you think it's going to get interesting or deep they skip along to something else. Then it starts this homoerotic undercurrent and then just ... ends.
I wouldn't even call it a good allegory on Scientology or other cults. It is almost worthless in that regard, there's only a few moments that show the malicious intent of groups like this, but then they swoop back to Phoenix acting disturbed again. I suppose I could say Philip Seymour Hoffman does a good job playing cult leader Lancaster Dodd. I wish he was the actual focus of the movie, but for whatever reason, the filmmakers decided not to do that.
Regardless, we spent a good hour afterward complaining about how bad this movie was, and that ended up being the best part of it.