I think many still hold Baylor in contempt not only on account of their actions during those "times", but also their actions after those events and occurrences.
The Baylor Board of Regents, Administration and fanbase largely did not come down or come out hard against what was happening and the culture at that time, IIRC. They were so intent on winning and to some extent were willing to ignore what was going on. And those people are still there.
That's how maybe I would explain Baylor then, and Baylor now. I could be wrong. I hope their culture has changed more than just on appearance only. Certainly the culture in their BB and FB programs seems pretty good now, largely due to the present coaches.