It's because tolerance is not what's actually being discussed. It's morality. No-one thinks we should tolerate rape or murder, or considers the locking in a box of those who commit those acts as being in any way intolerant, even though to a dictionary definition, it is.

It's just about changing morals, with the idea of tolerance as the vehicle that smoothed the way. All the dichotomies dissolve when things are seen for what they are.