It's not a new idea. I remember an episode of the Ghostbusters cartoon that had a town of werewolves and vampires battling (amusingly, whenever one bit the other, they turned, so it was an endless engagement). I can also count at least two occasions the Werewolf vs. Vampire thing popped up in Tales from the Crypt.

To a large part, I think World of Darkness is to blame. In Old World of Darkness (I know diddly about the New edition), werewolves are by nature spiritual creatures that thrive in wildnerness/nature, who hate humanity and cities in general. To werewovles, vampires are outside the natural order, thrive within cities, and are corrupting leeches, and are in part the sort of thing werewolves hunt to 'do their job'. And to vampires, werewolves are the boogieman that eat your face if you get too far out of your comfortable city.

Factor in Underworld, which was a ripoff of WoD and just made the two mortal enemies (Well, werewolves were once a slave to vampires, and the vamps did something to the werewolves which they seek vengence for or something)... Van Helsing also had the werewolf/vamp thing (well, one needed to be a werewolf in order to slay Dracula). And then Twilight, which has vampires (and then drags in the werewolves as an antagonist/opposite love interest)... But then, most of the "Supernatural Sexysexysexsex" books typically do that.

Ultimately I think it's sort of the supernatural (and more serious) equivalent of Pirate vs. Ninja. Some people really like vampires. Some really like werewolves. Some like'm both. They're cool. Additionally, they exist in the same general "Realm" (if vampires exist, it's not a great stretch to accept werewolves too and vice versa). So, people have a habit of putting two cool things in a grudge match to see 'em battle.

And let's face it. Practically anything relating to vampires OR werewolves today has practically nothing to do with folklore.

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