Though the conventional view of The Prince is that it promotes a supposedly amoral ideology for political leaders to embrace, this is probably not the only reason the religious authorities banned the book and condemned Machiavelli.
Machiavelli's intention was not so much to give prescriptions or directives to princes on how to rule as it was simply to describe, using many examples from both ancient and modern times, the actions that successful leaders have taken in order to obtain and hold power. In doing so, he revealed the hypocrisy, particularly regarding religion, of the European monarchs of his time and of the recent past. Machiavelli said of Ferdinand of Spain (without actually naming him) that "a certain monarch of our time presents himself as a defender of Faith and virtue but in reality is the extreme enemy of both." Given the violence, wars, and persecutions carried out not just by Ferdinand and Isabella of Spain but by the French and English kings of the time, all of whom represented themselves as devout, this statement by Machiavelli must have struck home with the religious authorities who worked hand in hand with these monarchs. Henry VIII's secession from the church in Rome as well as the Protestant Reformation had yet to occur when Machiavelli was writing. But both of these historical processes would simply have reinforced the general point Machiavelli was making about the violence and constant wars engulfing Europe, which were started and perpetuated by supposedly pious leaders.
It was Machiavelli's honesty about this overall situation that resulted in his being demonized not just by the papacy but by the European ruling class in general. He was made into a byword for evil by those who may have never read The Prince or his other works but were familiar only with a caricatured view of them.
The Pope banned The Prince by Machiavelli in 1559 because the book was considered a direct threat to Roman Catholic authority. Machiavelli proposes that a prince must have his own interests satisfied, even to the point of ignoring church doctrine...."The ends justify the means".This mentality could find itself in direct conflict with the church. The accepted views of morality as dictated by the Roman Catholic Church were of little matter to a prince. A princes loyalty was to the state. Machiavelli also suggests that a prince is above church authority.It is important to remember Papal authority had already been challenged throughout Europe by Martin Luther and the Protestant Reformation. By 1559 the Roman Catholic Church was fearful of losing power and authority to other religious groups. As a result banning anti church publications was done in hope of preserving church doctrine and authority.
In 1559, The Prince, as well as all of Machiavelli's books were banned and put on the "Index of Prohibited Books" list. The Catholic Church believed that Machiavelli promoted anti-Christian beliefs.
In The Prince, Machiavelli promotes a kind of deception. Politicians and leaders need not truly be moral, or good people, they only have to master the art of public image. As long as the people perceive the leader to be a good and moral individual that is all that matters. The politician need not be truly moral, but must be perceived as good and moral and caring for his people.