Benjamin does serve a purpose in the novel but he is not usually considered a main character. The main characters are Napoleon, Snowball, and Squealer. You could make the argument that scholars tend to focus on these three characters simply because they are the leaders of the revolution. And in this case, it is in the spirit of the novel to acknowledge the workers on the farm (Boxer for instance) to be equally as important as the leaders.
Benjamin does seem to be a supporting character, however, and this is because he is more of a commentator (sort of a cameo for Orwell himself or an outside observer) than he is an active participant. Benjamin is cynical and believes that, no matter what the initial tenets of the revolution are, the lives of the animals will not improve. In the end, he was correct.
Benjamin was the only animal who did not side with either faction. He refused to believe either that food would become more plentiful or that the windmill would save work. Windmill or no windmill, he said, life would go on as it had always gone on -- that is, badly.
In the end, Benjamin did try to save Boxer. And this does show that despite the intellectual cynic that he was, Benjamin did have compassion. Considering this and how Benjamin seemed to know that the revolution would fail, one could argue that Benjamin is a main character because he, more than any other animal, seemed to know how things would turn out. And although Benjamin knew or believed that things would stay bad or get worse, he does show compassion in the end when he tries to save Boxer. This suggests that as cynical as he was, Benjamin did care; he just didn't believe the revolution would work.