I think the obvious way out of this paradox is to recognize that tolerance itself doesn't carry any fundamental value, and never should have been thought of as something to value in the first place. The only thing that has fundamental value is good and bad feelings, like pleasure, pain, happiness and sadness (i.e. peoples’ well-being).

Oftentimes, tolerance can be a good rule of thumb, for instance, with respect to the way other people prefer to dress or talk, or what they do in private. But if some people behave in ways that actually hurt or abuse other people, then tolerance is obviously not the correct response.

Tolerance is just a heuristic. It's not a value unto itself. And if you think of it like that, there is no paradox.

That said, it’s worth mentioning that intolerance can take different forms, some of which should be encouraged, and some of which should be discouraged (i.e. not tolerated), depending on the context.

For example, if I see someone attacking another person, I might show intolerance of that behavior by physically intervening or by calling the police, which would probably be the appropriate response.

And if I see someone express an idea that I think is wrong or dangerous, although it would be wrong of me to express my intolerance of that idea by physically attacking the person, it should be seen as perfectly appropriate (and in fact, encouraged) for me to express my intolerance merely by engaging in a civil discussion in which I explain my opposing viewpoint.

It all depends on context. But what it still always comes down to is whether your actions are more likely to bring about more happiness and pleasure, or more sadness and suffering.