Female protagonists have safe appearances and personalities to be palatable to a wide audience. They want the viewers to relate and sympathize to them, limiting what they can do with them creatively. No such restriction exists for the villainous, as they can just go balls-to-the-walls with her design, demeanor, and personality. There's also a "tempting the hero" trope that is pretty common. Being literally seduced to the darkside.
If you're talking about why people on /co/ are attracted to them, it's because we like women that can/might harm us, and will almost certainly have control over the relationship. The degree varies depending on what type of villainess is being discussed. We enjoy the danger, the confidence, ambition, fashion sense, dominance, and sheer force of personality. It's the male equivalent of the "bad boy" attraction. We may, at times, feel like we and we alone could work our way into her heart and truly be beloved and, to an extent, possessed and protected by her. We think we can break through the shell and, perhaps, help her.