Does a wolf gain +1 hp / +1 skill by HD because he follow his favored class (animal) ?
Because actually, a wolf only gain 2 skill points at all !
So +1 hp/+1 skill by racial HD for creatures that follow just one class ( animal, construct ... )
Well, the bonuses were introduced to benefit characters who choose to specialize in one class; racial HD are not, strictly talking, a real class (although the rules often refer to them as "monster class" for easy reference), so I don't think it was the intended idea to give these bonuses to "plain monsters"...
Please also consider that a lot of monsters (dragons and outsiders come in mind) have already a huge amount of hp and skill points, and granting these races an additional bonus would be overkill, due to their high number of Hit Dice.
I'd say that racial HD don't benefit from favoured class bonuses.