Humans are creatures of cooperation. The NAP protects us against other beings (humans) which are capable of doing us harm. It serves us individually, and because it serves us individually, it serves us as a species.
Treating a bear as you would rather be treated is not a recipe for cooperation. The bear will still maul you. Treating a cow as you would rather be treated is not a recipe for cooperation, either. The cow will succumb to the food chain elsewhere.
Our intellect is not justification for slaughtering animals; ease of survival and enjoyment of existence is. Murdering a disabled person will not, in the society you and I live in, result in ease of existence or enjoyment thereof because, most likely, it'll upset someone who will want to do us harm.
Consciousness and suffering exist on a sliding scale, and it is likely that all life forms experience both in some capacity. If the difference between the suffering of a plant and the suffering of an animal is how well I perceive it, that's a pretty lame distinction to base my dietary choices on.
(Still not advocating for mass production animal farming; that's some wasteful nonsense.)