While Napoleon has clearly set up a tyranny backed up by a powerful "police state" in the form of the dogs, and a propaganda apparatus in the form of Squealer, Napoleon constantly disavows his power. His argument is not so much that he is in charge as that he is sacrificing himself to serve the needs of the other animals and the larger community. According to Squealer, Napoleon should be pitied and honored for all he does for the farm. If he needs to live in the farmhouse and have better food, it is only because of how much brainwork he does and how indispensable he is to the well being of the other animals.

Napoleon, of course, is actually producing nothing and living on the hard work of the animals, but he does the best to obscure this fact for as long as possible.

This is a difficult argument to make. For the duration of the story, especially at the end, Napoleon was in charge. No one came close. When there was an attempted rebellion, he destroyed it with a massive massacre. In light of this point, the only way that we can argue that Napoleon was not in charge is the end of the story, when he became a man.

That he became a man shows that he is still striving to become human. Hence, he is still subject to the worldview of men, not animals. Hence, we can argue that within his categories of thought, he still is shaped by the human world. So, if anyone is in charge, it is the human world. Admittedly, this line of reasoning is more philosophical and sociological.