This film IS NOT about Scientology!
It is about how authority doesn't always hold any...authority.
Freddie was a symbol of vulnerability after a tumultuous period in American history when many young men found themselves lost and disillusioned, looking for anything to latch onto. And The Master was just another opportunist, taking advantage of the current situation; a historical staple which has repeated itself over the eons.
Scientology is only one of many bull**** 'faiths' to prey on this sort of vulnerability, and it is the most relevant example only because it has persisted for so long.
But do you really think Hubbard was the only intellectual bastard savvy enough to come up with some vague explanation for all the things that worry us in this life, especially during that time?
This movie isn't condemning scientology. It doesn't have to. Scientology condemns itself.
This movie condemns arrogance, and the will to power.
"Buy the ticket, take the ride." --Raoul Duke, the great shark hunter