Exactly, but it is the deed that matters, not the motivation. The motivation itself didn't do anything. The action, by definition, did. Whatever the intent of the laws, they still have the effect of promoting some groups over others, because the penalty is heavier for crimes against some groups than others. Once again, action over intent.
Again, this law, which I oppose, doesn't support some groups over others. For example, any religious based crime would fall under it's umbrella, it's not limited to minority religions. Same with race and sexual orientation, though I acknowlege there aren't many assaults on hetereosexuals based on their orientation. If there were, they'd be actionable.