Nobody making movies quite understands the absurdity and the sacrifice of Faith like Martin Scorsese does. To believe in a higher power when all logic and reason points towards its absence is absurd, on the face of it and under its bones too - but even I, as a non-believer, can see that it's the leap (do not say "leap of faith," do not say "leap of faith") that is what they consider the Divine. It's the sound of voices echoing out of the emptiness - it is listening to nothingness and finding your answers inside of it.
Silence is almost entirely about coming to terms with that, and Scorsese has clearly wrestled with those questions his entire life - not just in his previous religious films like The Last Temptation of Christ and Kundun and his non-religious films like Bringing Out the Dead, but as a person, as a human being; the experience poring over these existential quandaries lives inside every frame of the film. (Sidenote: Roger Ebert's book on Scorsese talks a lot about the director's faith and I definitely recommend reading it.)
It is a serious and beautiful movie, thoughtful and moving and well-acted - one's atheism shouldn't get in one's way of trying to understand why people feel the need to believe, and what tolls it takes on them; what madness and beauty they find from their struggles with making sense of an inexplicable world. Scorsese makes religious movies for everybody, open to saints and skeptics alike - unlike the cloying "spiritual" treacle that often passes for "Christian Film-making" (I saw the trailer for The Shack the other day and nearly set myself on fire halfway through it) Marty's religion is all knotted up, an endless untangling series of questions without answers, of emotional turmoil and devastation and horror too, and those sensations translate to anybody walking through the door.