A lot is said about "tolerance" without actually defining it. But when you think about it, the difference between tolerance and intolerance comes down to this: Tolerance implies inaction, whereas intolerance implies action.
Intolerance is any time you take any action to make something stop. Whereas tolerance is when you leave something alone, and allow it to continue.
All other definitions are too fuzzy to use in a serious discussion.
And when we accept those definitions of tolerance and intolerance, it becomes obvious that neither is good or bad, because it always depends on the context.
For instance, companies are often proud to say that they have a "zero tolerance policy" towards sexual harrassment. So in that case, intolerance is seen as good.
And obviously, tolerance is often seen as good, for example, when we tolerate the existence of ideas we disagree with in our bookstores.
A "paradox of tolerance" is only possible if you have some assumption that tolerance is good to begin with. But it's not. Sometimes tolerance is good, and sometimes intolerance is good.
And what it mostly comes down to is this: we must learn to tolerate things that set a precedent for our own freedom, while NOT tolerating things that set an overall precedent for harm.