It is easy to give a theistic answer to the question in the title:
- Bad things should be avoided, and so it is likely that God would make rational beings dislike them.
- We tend to avoid things we dislike (this may even be analytic), and bad things tend to be detrimental to our fitness, so there is selection for dislike of bad things.
Of course some folks may say that there is no puzzle here, because our belief that these qualities are bad is caused by the fact that they are detrimental to fitness. However, that only answers why it is that there is a correlation between being believed to be bad and being detrimental to fitness, while the puzzle was about the correlation between being actually bad and being detrimental to fitness. Some of the folks I am imagining will go on to say that there is no such thing as badness, only beliefs about badness, and others will go relativistic and say that to be bad is to be believed to be bad. The problems with these options are obvious and well-known.
The sensible naturalist had better be a realist about the good and the bad. And then the correlation between badness and lack of fitness is, indeed, puzzling.