Why do vampires and werewolves hate each other?
According to many modern vampire stories, the vampire and the werewolf are natural enemies. In some stories it has to do with competition for prey, in some the werewolves exist to protect humans from vampires, and in others there is an ancient feud between the two factions that has continued through the centuries.
There's no right or wrong way to tell a story when it comes to vampire and werewolf fiction. If you think about it, these two make great enemies because they are both powerful creatures (especially at night), who are not known to have any other natural predators. Who better to stop a vampire than a werewolf, or vice versa?
Yet, there is a difference between fiction and myth. Myths may well be stories invented by ancient storytellers to explain the world around them, but at the same time there is plenty of evidence to suggest that many myths have their origin in reality. Perhaps it is a matter of perspective at the time, or a way for ancient people to explain supernatural events with their very limited knowledge of science. Either way, a fictional story can take whatever twists and turns it chooses, while a myth has more of a responsibility to maintain the perspective of the original story.
That said, on this site I try to limit the vampire discussion mostly to the concept of the modern vampire. By this I mean combining the various vampire myths across cultures and generations into one core concept of what a modern vampire would look like and how they would function. It would do us no good to include the various fictional vampire stories that have become hugely popular lately, because we know that these don't necessarily follow the rules of classic vampire mythology (I'm talking to you, Stephenie Meyer).
According to vampire and werewolf mythology, there really is no reason to believe that these beings have ever really had any interaction. There are no historical records of such events, and various vampire-based writings have no mention of werewolves whatsoever. I would think that if they were as big of enemies as modern horror authors suggest, there would be some consideration of them somewhere.
Of course, these are both creatures who endeavor to stay hidden from the human race, so who knows for sure if they have interacted or not? I'm not saying it's impossible, but I don't really see any reason to think that they hate each other, or even know each other. It does make a good plot device, though, doesn't it?