It's more of a rival apex predator thing then an actual hatred. Both are pretty equal in power, both are equally able to kill. It's more of a fight over territory and food then anything else. At least that's how I see the " hate " between the two, I myself out of instinct will rid my territory of any other apex predators so as to lessen the competition for food. Twas Underworld that spawned the popular idea that vampires and werewolves hate each other, but in reality the hate is no different then what's between a bear and a wolf in the wild. Both will avoid one another but will as well defend their territory from each other as well.
The crap that Harkon gets on with is more of his personal view of himself compared to others, not so much vampire compared to werewolf. Harkon is an egotistical psychopath that views himself better then everyone else.