This good Village Voice interview with Paul Thomas Anderson positions The Master among Anderson's other films, and Anderson downplays it as a Scientology expose.
So The Master is ultimately "about" Scientology in much the same way that Boogie Nights was about the San Fernando Valley adult-film industry of the 1970s or There Will Be Blood was about the California oil boom of the early 20th century. That is, it functions as a secondary concern, more setting than actual subject, more subtext than text. It is a way for Anderson to bring together an assortment of his typically idiosyncratic, iconoclastic characters and a conduit to larger themes of power and paranoia, domination and submission, free will and predestination. Indeed, no less than Anderson's previous film does The Master feel like a bold, somewhat cryptic meditation on underground forces that have shaped modern America. "Is it possible to live without some kind of master in our lives?" the movie asks, leaving it to us to decide.
For his part, Anderson is loath to see the movie as a variation on a pet theme. "Is it getting tired?" he asks when I say that Dodd and Freddie recall the surrogate father-son relationships in many of his films, beginning with the aging gambler Sydney (Philip Baker Hall) and his naive protégé (John C. Reilly) in Anderson's 1996 debut feature, Hard Eight. He prefers to think of his Master characters as unrequited lovers, a subtle, homoerotic tension that is triangulated in the film by the presence of Dodd's loyal, steely wife (Amy Adams). "But maybe that's just my way of dressing it up and thinking I was doing something different this time," he says.