My own theory is that it's because Machiavelli himself was a radical republican who was necessarily opposed to what the ruling class thought was polite, and The Prince is basically a blunt treatise on ruling class politicking and strategy without all the pretty lies about nobility or w/e that none of them ever really followed but liked to pretend they did. Not to mention it encourages things that are outright dangerous to an aristocratic system, like emphasizing that noble-on-noble conflict should be brutal and taken all the way to completion instead of treated with decorum and mercy.

Then liberals followed suit after liberalism subsumed the old aristocratic order into itself, so Machiavelli is the bad evil scheme man instead of the for-his-time-radical liberal who disrespected the old aristocratic system's norms.

Like I feel that the modern equivalent of The Prince would be if a communist agreed to write a guidebook for the Waltons in exchange for being allowed to return home to the Walmart corpo-fief, and it said they should be resolving their conflict with the Kingdom of the Mouse with PMCs and assassinations instead of the Corporate Court, and they shouldn't stop till all the Mouse's shareholders are dead, then they should give all of Disney's capital to the citizenry to buy their loyalty. Liberals would fucking hate that because it's so uncivil and gives the lie to their idea of a peaceful rules-based order.