Part of the problem with "black" connoting "bad" is not new, and part of it MAY be in response to the recent survey of preschoolers showing them 2 identical dolls - identical except one is white and one is black. When asked which one is good or loved, they chose white. When asked which one is bad or not loved, they chose black. The most disturbing thing was that the black preschoolers not only chose the black doll as the one that was bad, they identified themselves as looking that that doll and felt that they themselves were bad. So the idea of values being ingrained at an early age is very front and center. While black sheep wool might have been valuable at one time, certainly "the black sheep of the family" is not considered a compliment.
It's not always about being politically correct. It's about being sensitive, and about being willing to look at long-held beliefs.
A lot of nursery rhymes are scary or cruel (Jack and Jill get hurt - there's nothing wrong with the pail of water per se, it's that the rhyme is made with Jack falling down and breaking his crown, and Jill coming tumbling after. Again, with huge problems with kids getting concussed during sports, head injuries are on people's minds and they don't want to be dismissive, I think). A lot are based on old superstitions and unrealistic fears (same as saying "God bless you" after a sneeze). A lot are very sexist.
As noted below, "ring around the rosey" dealt with the plague. Others have to do with sudden death - "rock-a-by baby" or "humpty dumpty" for example.
Same goes for expressions we used to use and don't anymore because we know what they mean: To "gyp" someone comes from the idea of Gypsies as thieves (and since they are currently discriminated against, it's sensitive), "Indian giver" has long since fallen out of favor, and so on. Of course, "rule of thumb" is not used by many many people because it dates from it being legal for a man to beat his wife as long as the stick was no bigger in diameter than his thumb. With domestic violence continuing to be very high, a lot of people try to be more aware of antiquated ideas and not perpetuate those images.
So, with so many wonderful books and rhymes and stories abounding in children's libraries and even on public TV, and with many other old standards like Dr. Seuss available, it would seem we could make some different choices. What people do in their own homes is one thing, but what is done in schools and preschools needs to be sensitive to all of the children there and to teach values.