There isn't much controversial about Silence, at least as far as I can see, but it's a religious film that doesn't pander to religious people at all.
The problem, depending on how you look at it, is all the moral dilemmas of the film are based around the notion that bringing Christianity to Japan is a noble and important thing to do. You don't have to agree with that to get anything out of the film, but you do have to look at what's going on in terms of the character's believing it.
If you *don't*, it all falls apart.
Should Europeans be pushing their religion on Japan? Probably not!
Should you verbally renounce your faith and do whatever blasphemous things you're being told to do if it means stopping innocent people from being tortured and killed? Yes of course you f-ing should!
But I guess if you truly, deeply believe the truth and importance of this stuff, I guess these are difficult moral questions, and if you're willing to get inside the character's heads it's a pretty interesting film.
Garfield's greatest achievement is he manages to make the main priest quite likable and sympathetic, rather than a pompous deluded idiot. If he hadn't managed that the film might've been intolerable.