Non-human races got bonuses, because humans were the versatile Mary Sues that could do anything and be anything, while the demi/non-humans either couldn't be certain classes at all, or could only progress so far in the non-stereotrope classes. It was a balancing thing.

It worked on the Man is the Measure Of All Things trope, which they actually seem to love and don't want to break down any more than any other religious types who think Man is the tippy top of the Great Chain of Being (the Hindus' is no different, though instead of failures, non-humans are evil spirits that failed to be good at being human instead.)