Thomas Cromwell, adviser to Henry VIII, was well-schooled in "The Prince" and was single-handedly responsible for the irreparable demise of the freedom of the English people.
The first group to write substantially against Machiavelli were the early Jesuits.
Our Founding Fathers studied both of Machaivelli's famous writings in order to know the depths of evil power and to build a nation that could be immune to it all.
Saul Alinsky used "The Prince" as his inspiration when writing his books for the 60s radicals.
The modern embodiment of the implementing Machiavelli's evil power is the 44th president of the United States.
Cromwell saved England from monarchs and helped move it away from the papacy. Unfortunately England fell and went back into the slavery of monarchist rule.
As for the Jesuits disliking him, yes, they saw he was recording the method of the Borgias who he once worked for. His book was listed on the index of forbidden books precisely because it carefully documented the behaviors extant in the Vatican and the city states.
Machiavelli was essentially warning the world of what despots do and how they behave. He wrote from a view in the middle of it where he carefully was able to survive. He was tortured by the Medici family. He fell in with poets and writers. He never held high office as a ruler, and perpetrated no atrocities. His book was a warning about the kind of people surrounding him in renaissance Italy. Some Vatican, some from noble families running the city states.
Is a shame to see people believe he thought his prince was his dream. It was his nightmare.