I think that Orwell is most in sympathy with two of the major characters. They are Snowball and Boxer. He seems to think that the two of them are honest and are devoted to the ideals of Animalism (I also think that Orwell is in favor of Animalism as it was formulated by Old Major).
Orwell shows his sympathy for Snowball my emphasizing how he is always trying to improve the farm. He talks about how Snowball finds all sorts of things to read that help him figure out ways to improve things. He does not blame Snowball for things like the the disappearance of the milk the way he blames Napoleon.
He shows his sympathy for Boxer by always emphasizing how hard Boxer works and how selfless he is.