It is simple...

Because he won. The vampires were to destroyed to mount any true rebellion.

You have to remember that the Taney Court had made a ruling in Harker v. Tsepes that, as undead, vampires had no lives to lose, and therefore, could be killed with impunity as a means to protect the public health. This ruling seems incredibly inhumane to us, but remember, this was in the dark times before synthetic bloods like True Blood. The anti-vampire prejudices were more comprehensible during a time before modern anti-septics and blood transfusions.

It is also important to note that the South also featured their share of vampire hunters- Jonah Hex, for example. Not all in the Confederacy agreed with the notion of a vampire aristocracy. Rural lycanthropes were often fighting due to territorial bonds rather than any deeper solidarity.

Lastly, this part is glossed over in the same way that we largely ignore Darius Hellstromme's mass necromantic experimentation at the Andersonville POW camp. Many Americans like to cling to a romanticized notion of the civil war as being purely about noble knights doing battle in their steam-power airships, and forget that the ground war frequently involved a terrifying nocturnal war of vigilantism and vampirism.

Oh yes, my sources: Leone, Pale Riders: Vampire Cavaliers of the Old South; Back East: The South by Shane Hensley; Peter Allison, Merrimack vs. Monitor: How American Airship Combat Prefigured the Dystopian Wars