The movie is set in 1637 when the Tokugawa shogunate decided to wipe out Christianity. They begin a search for "Hidden Christians" and priests. The movie opens with priests being crucified and tortured. This is not a samurai movie in the traditional sense, but it is about the samurai era, and it does show how the samurai culture was all about control.
In Macau we have a Jesuit priest telling two younger priests that their mentor, Father Ferreira, a missionary in Japan, has renounced his faith. The younger priests Rodrigues and Garupe do not believe that this could be possible, and decide to head off the Japan to find the truth. When they arrive they find Japanese Christians hiding their faith and living in fear. A samurai who is in charge of the search for Christians, called the Inquisitor, ties some Christians to crosses near the ocean where they will eventually drown.
Rodrigues is captured, and the Inquisitor explains to him how Christianity is something that is just not good for Japan. Rodrigues is then brought to the beach where he sees Garupe refuse t o renounce his faith which results in three Christians being drowned in front of him. Garupe also drowns trying to save them.
Rodrigues is then taken to a Buddhist temple where he meets Ferreira who tells him that Christianity is not meant for Japan. Rodrigues is then forced to renounce his religion in order to save Christians who are being tortured.
Rodrigues and Ferreira then work for the Japanese, finding Chrisitian items being smuggles in by traders. Years later, at his death, we see a small cross in the hand of Rodrigues.
I really thought this was a great movie. It showed how religions were (and are) suppressed. The Japanese felt that Christianity would make the Japanese less "Japanese" and would make them more susceptible to the Portuguese, Spanish and Dutch. The Spanish Inquisition, Stalin, Hitler and Muslim imams all saw dangers in having their people embrace outside religions. They would lose control if they did.
I think Scorsese is saying that religion should be a private thing between you and your God. Forcing someone to take on your beliefs is obviously not something God would want you yo do.