What is Machiavelli's perspective on human nature and free will (the will of the ruler versus the will of the subjects) in The Prince?
I would suggest that, at least where The Prince is concerned, the will of a ruler's subjects does not much enter the equation at all. This work is first and foremost written from the vantage point of the rulers, as it addresses the question of how power is most effectively wielded and maintained. In this sense, Machiavelli speaks very little from the perspective of the ruled; this should not be entirely surprising, given Machiavelli's focus on power. After all, aside from the extremely risky option of rebellion, or perhaps through various measures of non-compliance, how much real influence or agency can most commoners be expected to assert within a monarchical system of government?
Ultimately, then, for Machiavelli's analysis in The Prince, the only will that truly matters is the ruler's, and so long as a ruler follows Machiavelli's advice, they should expect that the risk of rebellion on the part of their subjects should be mitigated and contained (at least, this is what Machiavelli would have them believe). Of course, at the same time, Machiavelli is clear on his assertion that the prince can never enjoy absolute control of his political destiny: indeed, as he suggests in chapter twenty-five, "Fortune is the arbiter of one half of our actions.." By this assertion, much of political reality ultimately lies beyond any one human being's ability to control. This is precisely the reason why Machiavelli places such a focus on political decisiveness: since so much of politics are outside of a ruler's ability to directly influence, this means they need to be actively engaged whenever the unexpected occurs, whether it be to take advantage of opportunity or to mitigate potential dangers.