I've read the books, and seen the movie... the impression that i walked away with was that it was about not blindly following authority.
Its about a corrupt power that tried to tell people how to think.
Its mostly using the spanish inquesition as an example...(something that is described as the most evil act of man) the catholics are angry because they were responsible for that, and they don't want children to question whats right or wrong in their leaders.
I find it ironic that there response it to try and silence the movie.... proving its point entirely right!
LOL