True, they have a bad reputation. But in the A&E Pride & Prejudice, Mr. Darcy rides a black horse, so they can't be all that bad
I guess dark colors are just associated as wanting to blend into the shadows because one has something to hide...or something like that. Therefore dark-colored horses are chosen by people with things to hide, who are most often villains.
How's that for a strange qualification of the plight of black horses?