But yes I know what you're talking about: that is certainly a behavior of a certain type of racist I've encountered. I find quite often that people with reactionary beliefs feel that they are personally under attack, or at least its important that they nurture a certain type of victimhood. I must insist, though, that there is another type that comes from a belief that your perceived "genetic" (here in quotes because these people tend to play very fast and loose with that word) inheritance make you in some way implicitly superior to people who lack your "genes". It's for this reason that I bring all of this up: no matter what they say, there is a difference between wanting to relegate people of color or gays to a second class in society and the intolerance of those beliefs. It's this relation that Popper was talking about.
I also want to be clear that I'm not trying to say what you've experienced isn't real. There are definitely people like this. My reply was only in the context of the top-level "tolerance of intolerance" quote.
On the other hand, I am pretty convinced that my genetic inheritance makes me "superior" (in some vague, but obvious way) to a cat- and yet I've never harmed or desired harm for cats- I actually like them. Or, to make a different example, while we consider it unacceptable to think of race X to be "superior" to race Y, we have no particular issues in admitting that the individual Albert Einstein was "superior" (again, in some vague way) to many other individuals (us included)- and yet from that doesn't follow we mean those individuals any harm or disrespect.
Btw, we have an entire genre of fiction (a subset of science fiction) in which humanity is threatened by technologically and cognitively superior races coming from other planets- this doesn't prevent us from trying to exterminate them to ensure our survival.
Would they use the words "free speech" and "tolerance"? Probably not. But "standing up for yourself after being attacked unprovoked" and "justifiable intolerance of intolerance" are the same argument, with only superficially different wrapping.