The first perspective is one of the Christian believer, while the second is of the atheist.
In short, the movie is about how obstinate stubbornness is always a virtue when practice by "us" for our beliefs, and always a vice when practiced by "them" for their beliefs.
For the Christian, Silence is a simple movie about how obstinate stubbornness is a virtue, because it is the ultimate test of faith in the face of extreme persecution. For the Christian, this movie is the Christian equivalent of the World War II movie "Unbroken," about Louis "Louie" Zamperini. Both movies are examples of the heroic courage and resolve of people who refuse to be broken, even in the face of ultimate cruelty and suffering. While Zamperini's story is a true one and Silence is based is historical fiction, both stories are variations of the biblical story of Christ, or what Joseph Campbell called "the monomyth."
The monomyth is an idea detailed by Joseph Campbell in his seminal work of comparative mythology, The Hero with a Thousand Faces. Written in 1949, Campbell explains that the monomyth is a story that has been repeatedly plagiarized over the centuries, of a "hero" who overcomes "fabulous forces" and returns from his harrowing adventure "with the power to bestow boons on their fellow man." Countless examples of exist besides the Jesus story, including Osiris, Prometheus, Moses, and even Buddha. Hence, there really is "nothing new under the sun," as it says in Ecclesiastes 1:9, for every new belief is simply the retelling and repackaging of a belief that preceded it.
Like Christians who allowed themselves to be fed to the lions in Rome, holding fast to a conviction is the highest moral virtue for the "true believer," even if such "believers" see it as a vice whenever anyone else is equally as stubborn for their secular or even non-Christian beliefs. The implicit underlying assumption of the "truth" of Christianity, along with the implicit assumption that everyone else's "truths" are actually lies, goes unnoticed by the Christian, of course. Just ask Tomás de Torquemada,. the "Castilian Dominican friar, and the first Grand Inquisitor in Spain's movement to homogenize religious practices with those of the Catholic Church in the late 15th century, otherwise known as "The Spanish Inquisition."'
If Torquemada had been raised a Buddhist in Japan in 1641, instead of a Christian in Spain a century earlier, his underlying assumptions would surely have been reversed, leading him to assume that the Christians he was torturing to death were the real "heretics" to the irrefutable truths revealed to him by the divine Buddha. In this respect, Fr. Rodriguez cannot see that the Japanese Inquisition that he is being subjected to is simply a reflection of the Catholic Inquisition established to stamp out heresy in 1562, and earlier by Pope Gregory IX in 1232. Beliefs for the ardent believer, like bloodlines for the Aryan, must be kept pure, whether they are Christian or Buddhist or whatever.
From Muslim Extremists to Native Americans to Protestants to Buddhists to atheists and beyond, "believers" in one religion or another, only ever recognize the virtue of being obstinately stubborn for a "belief" when it is their own belief they are being stubborn for. For everyone else, such stubbornness is only ever seen as a "hardening of hearts" agaisnt "the truth," and thus a vice. That this only encourages ever greater cruelty to be imposed to "test" the validity of one's claims is overlooked equally by all. And the fact that even St. Augustine believed that those who converted to Christianity under torture were often the most ardent believers of all, only encouraged the use of torture as a legitimate means of testing one's faith (which is why some today even practice self flagellation for their faith) and of enticing conversion.
With regards to the virtues and vices of stubbornness, one need only glance at the Old Testament to see that the Jews were hated by the Romans for exercising the virtue (or vice, depending on your perspective) of being just as obstinately stubborn as the Christians would be centuries later. In his memoirs, for example, the Roman Emperor Hadrian expressed his overwhelming frustration with the Jews who, despite his own efforts to accommodate them as best he could without loosing the respect of his fellow Romans, and more importantly his superiors, had devoted themselves to an extreme dogmatic inflexibility with regards to their beliefs. Hadrian wrote repeatedly about how, time and again, he could not fathom why the Jewish beliefs seemed to produce little besides such obstinate stubbornness.
From an atheist perspective, on the other hand, Silence is a fascinating look at the human mind and the power of a belief, especially our devotion to the certain brand of a belief we were born into, even if the underlying story of our beliefs is roughly identical to the beliefs we are opposing as "false" or "evil," like Buddhism is to Christianity.
That the Buddha was to feudal Japan what Christ was to medieval Europe was simply proof of the very limitations of human understanding that Fr. Rodriguez is unable to accept, because of the hubris of his own faith. Indeed, his hubris, which he only interprets as his "humility," alienates him from being able to see the similarities between his Christ and the Buddha. Instead, he has nailed his ideas and his perspective to the cross of a particular "belief," which he no longer considers to be simply his own subjective interpretation of "truth," but is a "truth" itself; one that he feels the salvation of his eternal soul now precariously depends.
For Rodriguez, his obstinate refusal to look at things in a different way is a virtue, even though the recalcitrant teenager is always condemned for behaving in exactly the same way. And even though others are being tortured and killed because of Fr. Rodriguez is being as recalcitrant as a teenager for his faith, he appears to feel that it is his captors refusal to accept his Christian religion this is the true vice, and the true cause of their sufferings.
Indeed, the priest even proudly proclaims that "the blood of martyrs is the seed of the Church," which is a phrase any extremist today would whole heartily agree with, from ISIS to Branch Davidians to Jonestown to the followers of Warren Jeffs. Here, all would-be martyrs stand on equal footing, whether they are asked to murder their sons like Abraham was asked to knife Isaac to death, or like Christ who was willing to be brutally tortured and murdered to death to establish the supremacy of his own religion.
Rather than simply following the example of the Donmeh Jews, who at the same time historically, circa 17th century, where converting to Islam publicly in the Ottoman Empire while continuing to practice their Judaism privately among themselves, the Christian priests in Silence feel the need to prove that they are right, and that their beliefs are stronger than that of the Buddhist inquisition that is torturing them. How ironic. And in this way, Christianity had perhaps how done the Hebrews of old in terms of their stubbornness.
But dying for one's beliefs is not a virtue, it is is vice. Christ did not die for his "beliefs," in other words, but because he sought to defend the powerless agaisnt the dogmatism of religious extremists called the Pharisees and the Sanhedrin. Anything other than that is simply spiritual hubris masquerading as religious humility for a brand name.
[i]. Joseph Campbell. The Hero with a Thousand Faces. Princeton: Princeton Univ. Press, 1968, p. 30 / Novato, California: New World Library, 2008, p. 23.