The villains in Animal Farm would have to be the humans and the pigs, such as Napoleon and Squealer. In Old Major's initial speech to the animals in Chapter 1, he outlines how humans are the fundamental enemy to the animals:
Why then do we continue in this miserable condition? Because nearly the whole of the produce of our labour is stolen from us by human beings. There, comrades, is the answer to all our problems. It is summed up in a single word--Man. Man is the only real enemy we have. Remove Man from the scene, and the root cause of hunger and overwork is abolished for ever.
Human beings are seen as the source of all exploitation on the farm. Old Major draws the picture of how human beings are responsible for the animals' suffering and thus, they are the fundamental villain. The way in which Jones brutalizes the animals and mistreats them would help to make him a villain.
As the revolution takes place, the pigs become the leader of the animals. Within the pigs, a power struggle takes place between Napoleon and Snowball. Napoleon is more motivated by power, while Snowball is more devoted to the tenets of the Animalistic revolution. When both contest for power, Napoleon is able run Snowball off the farm and consolidate all power for himself. As Napoleon and Squealer, his minister of propaganda, gain greater power, they resemble the humans in their desire to silence the voices of the animals and exploit them for their own benefit. Their use of the dogs to maintain control becomes evident and quite brutal as a means of repression.
In this regard, the pigs become villains. The animals are conditioned to simply accept such a state of being in the world. As a result, they are not able to successfully rise against Napoleon. Those who do face a brutal and painful end, as seen in chapter 7 with the Minorca pullets and other animals who are perceived to be "enemies" of "Comrade Napoleon." The manipulation of power and the ability to be indistinguishable from human beings is what makes the pigs such as Napoleon and Squealer the villains at the end of Animal Farm. The ending scene in which the animals are on the outside looking in at both of their oppressors is reflective of villain status being conferred on both the pigs and the human beings.