Compare how Mr. Jones and Napoleon ruled the animals.

In the beginning, it would seem that Farmer Jones and Napoleon have a very different approach to the treatment of the animals. While a farmer would typically care for the animals on his farm because they are necessary to keep the farm going and to make money, Farmer Jones is very careless with his animals. In his alcoholic state, he forgets to feed and care for his animals, leaving them in poor conditions. Napoleon, in contrast, seems to have the best interests of the animals in mind, and proposes to take care of and ensure the well being of all animals on the farm.
However, as the reader moves through the story, it is at first foreshadowed through the taking of the milk and the puppies, and then blatantly seen, that not only does Napoleon not care for the animals, he has a brutal, dictator mentality that forces the animals to work harder for worse care than they had with Farmer Jones. Napoleon seizes the opportunity to manipulate the animals into submission and sets himself up as the ruler.
Being a farmer, one would expect Mr. Jones to treat his animals as animals, expecting them to work and controlling them. In return, the animals should expect to be fed and cared for. As an animal, Napoleon should have had a respect for the work of and care for the animals. Because of Napoleon's approach, it would seem that his treatment of the animals was far worse than that of Farmer Jones.

There are close similarities between the respective regimes of Mr. Jones and Napoleon. For one thing, they share a profound contempt for the animals on the farm, ruthlessly exploiting them for their own selfish gain. The main difference, however, lies in the fact that Napoleon is a good deal more ruthless and efficient at exploiting the animals than the alcoholic Mr. Jones. And yet Napoleon is an animal himself!
Mr. Jones treats the animals badly because that's just how it's always been. As far as he's concerned farm animals exist purely as a food resource for humans. There's no ideology involved here; Mr. Jones is a farmer, and the animals are there to be used for food and profit. That's how the farm has always operated. Humans are in charge, and the animals do as they're told. If not, then Mr. Jones can always rely on his trusty whip to keep them in line.
Napoleon, on the other hand, looks upon the animals as a source of political power. Having driven Mr. Jones from the farm, he sees a great opportunity to establish himself as dictator. Napoleon's desire for total control is based on a deeply cynical attitude towards his fellow animals. As an animal himself, he knows what they're capable of if given a chance to run their own affairs. This is something that Mr. Jones would never be able to fathom in a million years. Yet instead of joining with the other animals to build a genuinely Animalist community in which everyone works together for the common good, he chooses to dominate, control, and exploit to satisfy his own lust for power. In other words, Napoleon, unlike Mr. Jones, really should know better.