In Greek mythology, Hecate was a sinister goddess associated with the underworld and magic, usually of the evil sort. Sorceresses like Medea were in league with Hecate, and there were all sorts of spells and incantations directed to her in the practice of magic.
It was believed that Hecate was active at night (naturally), and that she often appeared at crossroads, sometimes accompanied by hellhounds (whatever they were), and perhaps even had a hellhound head herself. But, alternatively, Hecate was often said to take the form of a cat—black, of course. Considering what a sinister goddess she was, it isn’t hard to see why the Christian Church might form a low opinion of black cats, given their connection with this goddess of night and sorcery.