Note: partially based on a similar post on TVTropes.
I'd like to note that the Rebels (or some of them) seem to be extremely racist. In the quest that allows oyu to get the Zoltan ship, if you choose the Stop this! You're killing everyone! dialogue option, they'll respond something like:
No. It doesn't matter how many innocent people, human or otherwise, we kill. Humans must unlock their full potential; the Federation treats all races as equal! 14/88 human supremacy NOW DIE FEDERATION SCUM!!
One more reason to hate the Rebels, besides being arrogant pricks, marauding bandits and changing a working galactic federation into a chaotic something else.
So, from the start: who are the Rebels?
We know they possess an arsenal of fairly advanced ships of several classes. Auto-Scouts have advanced AI (and, in some cases, a cloak), Fighters and Riggers are available in healthy numbers and are quite well-armed, and the Flagship has rechargeable Zoltan-pattern supershields. We can also assume that their cruisers may be as well-armed as the Federation Cruiser because they easily scare off the player ship of any class regardless of shielding and evasion. An Artillery Beam can do that.
What this means is those aren't just farmboys. We're dealing with a force capable of taking on the Federation in a stand-up fight. Yet they are as marauding as any revolutionaries, who have a tendency to carry more weapons they would possibly need and go grab some stuff. Basically, Russian revolutionary sailors and soldiers in space. Still, they're a military.
Also, how many times have you seen a non-human Rebel? I might have run into a Rock-crewed Rigger but it may have been a Pirate. So, racial purge. It's less pronounced than it used to be, apparently.
Additionally, consider the Engi Brigade. There are racial formations in the Federation battlefleet. By definition a federation gives each subject territory (state, republic) some autonomy. It used to be an Empire in one of the earlier builds. Now, what happens when the Rebel Flagship is destroyed? Complete and utter screw-up. Just from their ilitary command being blown up.
As to Federal races, we know the Rock and the Engi (and the humans) are certainly members. The Fed cruiser also has Mantis crew, but we also know of a Mantis-Federation War.
The "Rebels" are a military coup with racist undertones who've swept up a lot of shadier types, and a lot of Rebels don't mind making a profit.
Star Wars Imperials are now the Rebels, and the Rebels (post-film) are the Imperials. Even funnier when considering the Old Republic period: a small Empire tears the complascent Republic a new one through skill and subterfuge.