Tom Cruise blows up Scientology?

Rating: 10/10 (24 May 2013)

First of all this film is an excellent sci-fi, very well put together, and I really enjoyed it.
I only started thinking about deeper meaning of the film, related to private life of Tom Cruise, when I saw the very end, when Tom returns to a woman and daughter looking almost like ex-wife Katie and Suri, and saying he is where he belongs, home.
Before this happened, he destroyed an upside down pyramid with an eye inside, flying in space, who he first thought were friends but brainwashed him. Scientology is about aliens coming to earth bla bla, if I am not wrong?
The woman put to work with him looks like Nicole Kidman, red hair, etc, but it turns out only forced by the evil aliens. They live a perfect life, but Tom dreaming about living in a cabin by the lake. With the other woman. Looking like Katie.
Is Tom regretting something because of loosing Katie?
What I do not get, what it means flying around in a jet, looking like a male genital. Being a sex symbol?