I think that Napoleon can operate as the antagonist in Orwell's work. I think that authority structures in all of their forms seem to be the antagonist in the novel. Napoleon is part of this, but in the larger sense, there is a view of government presented indicating that it will always become larger and more constrictive of individual rights to suggest that all authority is an antagonist to citizens' well being. The humans are seen as a proverbial enemy, and while Napoleon and Snowball compete for power, there is almost a picture present that either one would become a victim to their own power because of the lack of institutional check or control. In this light, all authority structures seem to be set at odds with a sense of individual happiness or contentment. Napoleon is part of a larger configuration that is designed to prevent a full realization of human happiness and self- actualization.
I think that this is a matter of opinion since, in this story, there is not really a clear protagonist. In my opinion, the real antagonist in the story is Napoleon.
I say this because I think that the main conflict in this book is between those who are exploited and those who do the exploiting. This means that, for most of the book, the conflict is between all the animals of the farm (except for most of the pigs) and Napleon. I think that the majority of the animals are seeking freedom and liberty. I think that Napoleon is the antagonist because he is the one, for the most part, who is preventing them from achieving that freedom.
I think the antagonist in Animal Farm is Napoleon because of his attitude towards the rest of the farm. In the first half of the book though, this was not clear. Once Napoleon took leadership over the farm, he acted as one of the other animals would but, eventually he began to show how he was the antagonist.