I'd never use that description -- to me, the Confederate cause was repulsive and the Mal Reynolds character seems like the kind of person who would see that. But if someone has a warm spot for the confederacy I guess I can see that point of view.
I would prefer not to get into a long discussion about the War Between the States, but I happen to believe that the "Confederate cause" was essentially that a group of states wished to leave a union that no longer represented their interests. The other side was fighting to transfer power from the individual states to the central government.
You may disagree with that outlook about our own civil war, but is this the general framework behind Firefly?