What the hell is up with Tom Cruise movies? Most of them are about where he uncovers a government conspiracy, then realizes he's not who he thinks he is, then restores his true identity. And these are big budget productions.
I think the scientologists are funding these flicks as recruitment tools. They stir up distrust in government, then they replace identities with alien worship or something. I bet if you go back and watch these movies, there are some subtle references to scientology at the climax, where the hero wins.