I hate to describe them in such absolute terms, especially since the game has you take part in missions involving killing them both, but I think the game has you being hated by the Haitians more after all is said and done. If you're just playing neutrally, the Haitians should hate you more than the Cubans do, since you end up killing more of them assuming you're playing normally. Then again, the game does seem to have you in more missions where you're on the Cubans' side killing Haitians. Am I right, or could it really go either way?
I suppose the Haitians are the more unfriendly bad guys, or as least are written and programmed as being more antagonistic and randomly violent ( I would have preferred to have never worked for them actually, I feel the same way about the Mexican government in "Red Dead Redemption").