It's because black cats are often overlooked and even vilified. It's not uncommon for them to be the last kittens left when their litter mates have all been adopted. Some of this is because, being black, they tend to disappear into the background. They're notoriously hard to photograph in a shelter setting, and they don't have the facial markings that animate their tuxedo-marked friends.
Even folks who don't actively admit to fearing bad luck from a black cat crossing their path sometimes hold back from adopting them. It's an odd idea, born of the middle ages, that associates color with virtue. White is considered pure, so the opposite must be... Yeah, stupid when phrased like that, but still pervasive in the culture.
In our house we have a tradition of keeping black cats around. Gabriel already had Lucy (a quirky, loving, male kitty) when I moved in with him, and several years later we found Fredo living off pizza crusts in an abandoned apartment. Turned out that the girl who originally had him moved and left him behind despite naming him "Hero". We took him in and changed his name, making him our very first rescue. He lived with us for 17 years.
Whenever someone asks "what's the harm in having a couple of little superstitions?" I always think of black cats. Superstitions and lazy thinking can do active harm when they make it culturally okay to mistreat or dismiss individuals based on superficial identifying characteristics. And if it seems like this is applicable to more than just cats, you're right.
Superstitions can be insidious. No one is free of them. But I can assure you that black cats are not bad luck. If they are, I'm pretty screwed. Because this is my latest tattoo.