The only form of intolerance Popper recognized was bigotry around beliefs. The concepts (and words) homophobia, racism, transphobia, and islamophobia were not even invented when he wrote about the paradox of intolerance.
When he described the intolerant, he specifically meant people who would use violence to stop others from expressing different beliefs - nothing else. He did NOT mean "intolerance" of any particular skin tone, or sexual behavior, identity group, etc.
This is important because intolerance of sexual behavior doesn't structurally break the system of discussion and truth-finding that we use. You could jail every blue-eyed person, just was we jail people who commit certain crimes, but as long as everyone can speak then our system for collective truth-seeking still works. The ONLY meaning for the word "intolerance" that breaks that is intolerance of free speech, and that's the only kind of intolerance that Popper said needs to be suppressed with force. And he was right.
I see this misunderstanding constantly online - honestly it's hideous to see people twisting Popper's pro-free-speech message into an excuse to crush those they misunderstand or disagree with. Literally inverting his meaning.