This is a difficult question and therefore one definitely worth asking. I'll give my thoughts on it but would invite others to chime in. In fact, you may want to post this as a discussion point as well because you're more likely to get multiple responses and there's going to be different responses to this question.
It is not "fair" if certain classes or groups (in the case of the novel, certain species) get to make the majority of decisions for a society in which there are other classes and groups. In an ideal democracy, everyone votes on everything.I'm not sure that such a democracy exists in the world. There are democracies but they tend to be like America's democracy where we vote for representatives and they do most of the decision making. (America is more of a republic.) Although it is not fair, it is generally agreed upon that it is wise to have the smartest people making decisions which have complex implications on all aspects of our lives.
That being said, just because a person or persons are smart doesn't mean they are ethical and altruistic. Snowball seemed like he retained his ethical values and the original spirit of the rebellion which was to make all animals equal. However, Napoleon (just as smart as Snowball) let his own power corrupt his values, if he had any in the first place.
In fact, despite what I said about it being "wise," in many cases it is not smart. This has been true throughout history. When an elite group, or one person, has control over a nation or an economy they/he/she looks out for their own interests. Orwell suggested a solution of a mix of democracy and socialism, in which the majority (the working class, or in Animal Farm, all the animals) would run the economy. Thus it would be socialism emerging by itself out of an already established democracy.
At the risk of sounding hypocritical, it is wise to have the smartest people making important decisions, but it is not wise to allow them to have this power without repercussions for the decisions they make. That power must be kept in check. The cliche is that absolute power corrupts absolutely. Notice that one of the ongoing debates between Republicans and Democrats is the power of the central government. Republicans think a Democratic style government has too much power. Democrats think Republican governments lack of centralized power gives too much power to banks and the richest one percent of the population. In either case, each side is arguing that there is too much power within a small group of people.
So, back to your question again, is it fair? History has shown that no, it is not. We are still waiting for a foolproof way to keep all forms of power from becoming too great.