The New York Daily News reports that, specifically, Cruise's major issue with the movie is the suggestion that L. Ron Hubbard made the whole thing up about Xenu and thetans. No, really. According to the paper, one scene in the film shows Philip Seymour Hoffman's Lancaster Dodd (who is modelled on Hubbard) ruminating on The Cause, the religion he has founded, only for another character to claim he's inventing it as he goes along. Here's how the paper describes the sequence:
According to our insider, one scene that didn’t sit well with Cruise takes place on a patio where Joaquin Phoenix, who plays Freddie Sutton, a troubled drifter who becomes Dodd’s right-hand disciple, watches Dodd pontificate about the religion he has created.
During the scene, the source says, another character close to the founder turns to Phoenix and says of Dodd, “You know he’s making it up as he goes along.”
Referring to the actual Church of Scientology, our source says, “Tom Cruise’s people are grumbling about this line — amongst others — but Anderson is not taking it out.”
And add that to the final scene of the second teaser of the film, where Freddie Sutton angrily exclaims, "I know you're trying to calm me down, but just say something that's true!" and it seems to indicate that Dodd is being established as an ambitious, if not entirely trustworthy individual.
Thus far The Church of Scientology has no comment on the movie as they haven't seen it, but it should be noted that according to famed defector Marty Rathburn, the religion's organizers are instructing members on how to crack down on "rumors" about them that are swirling around the TomKat divorce. And as the October 12th release date for "The Master" draws closer, and particularly as more details about the movie are revealed, we wonder how Scientology will react to the film officially, or otherwise. Guess we'll soon see.