He continues to do intolerant stuff: https://rms-open-letter.github.io/appendix
Yes. RMS argued for gender-neutral pronouns since more than twenty years ago. Just because it is a different set of neutral pronouns than is popular today, some people mark him transphobic. That is absurd.
Unfortunately, the more tolerant attitude of just agreeing to disagree seems to have gone out of fashion. Now the preferred option is to destroy a person's entire career and slander their reputation with deliberate misinterpretations of what they've said and done.
Being "intolerant to intolerance" is a fairly well accepted idea in societies that value personal freedoms.
It still looks to me that in this case, it's the people calling RMS intolerant that are the intolerant ones. On the contrary, I think RMS actually tolerates a whole lot. He clearly has different views than others on a variety of topics, yet he doesn't let it affect his technical decisions. He's been attacked viciously in the media, but he's tolerated it and is coming back to the FSF. An intolerant person would disappear. Consider all the people on the board of the FSF with opposite political views than his, that he tolerates on a day-to-day basis. An "intolerant homophobe/transphobe" would not tolerate having homosexuals/transexuals on the board, for instance.
He'd also have been disgusted by being used in a propagandistic manner.