So, when Popper doesn’t tolerate intolerance,
he is being mean?

Intolerance is something no one should tolerate.

From where I’m looking, intolerance is like a pebble in your shoe. You may walk for a while, without removing the pebble, but the damage will be there. For certain.

And if you persevere, the damage will be permanent.

Your question is a tricky one. Popper is not necessarily mean when refusing to tolerate intolerance.
He would have been mean only if he used unkind words when trying to convince the intolerant to change their hearts.