Silence is one of Martin Scorsese's finest films, which is really all that needs to be said about it. It's not as masterfully paced as Goodfellas, as carefully plotted as The Departed, nor as vibrant or politically thoughtful as Gangs of New York, and it doesn't have a seismic performance like DeNiro in Taxi Driver or Raging Bull. But the film is an utter masterpiece through and through.
Silence is about faith. It does not lend itself to pat readings, but I think some explanations are better than others.
The very core principle of the film is that faith is deeply personal and should be respected. But Silence is a a great film because it goes beyond that: Scorsese delves into the question of how should one react when the deep underlying tenets of a religion conflict with cherished practices and commandments. This question could not be more relevant today to debates in the Pope Francis era of the Catholic Faith or for questions regarding the modernization of Muslim practices. Scorsese comes, correctly in my view, with a preference for underlying principles over practices and specific commandments.
Let me explain why this is the position he takes. First, Father Rodrigues often tells others to apostasize. But he holds out himself: he sees himself as a martyr figure. We tend to take his point of view, but when Father Ferreira tells him that this view is arrogant- that comparing oneself to Jesus is immodest- this is a powerful rebuke.
Second, Father Garrupe did not apostasize and his fate is telling. He desperately swam out to sea to save those drowning. But all he does kill himself while not saving the other. His body floats in the water, face down. His is not the death of a martyr, but the death of a man who impractically failed to renounce his faith to save others. Standing from afar, Rodrigues wants him to give in. He can see that it is stubborness and to some extent self-importance for Father Garrupe not to make this mental and spiritual sacrifice, but he cannot yet see this so plainly when he finds himself in the same situation.
The ending is also telling. I have seen multiple criticisms of the coda to the film: Silence keeps going for 15-20 minutes after the dramatic event of the film has passed. Scorsese is a man who knows how to end a movie: you can't be one of best directors of all time without that skill. He has shown himself willing to end a film immediately after a startling burst of action (The Departed), after a dramatic event with a short and surprising coda (Taxi Driver), and conventionally but incredibly effectively (Raging Bull, Gangs of New York, The Aviator, and Hugo). It is noteworthy that the other Scorsese which drags on longer than expected towards the end of the film is his other film about the Christian faith: The Last Temptation of Christ. The dragged out ending in Scorsese's 1988 film is about Jesus's last temptation.
All of this is to say that Scorsese carefully works on his endings. Scorsese didn't haphazardly plot the last 15 minutes as some critics suggest because Silence was a long-in-the-making passion project of the director.
Rather, the film's conclusion is a careful demonstration of the fact that you can take the man from his faith, but you can't take the faith out of the man. A man can still believe even if he does not follow all of the formalities of his religion, so long as in his actions he stays true to the spirit of his faith.
An essay could be written about virtually every character in the movie, all of whom are deeply human. Silence also has important things to say about the tradeoffs between religious freedom and societal cohesion and the balance between blind faith and empathetic tolerance which could spawn tomes of scholarly debate.
More than anything, however, Silence is a devastating reminder that religion is a human exercise meant to benefit the people who have inhabited or will live on this Earth. We may not agree on the deities we pray to, the stories behind our religion, or even many of the principles that underly our beliefs. But we should all agree that we are our brother's keeper.