I'm not sure about transphobic, as that allegation did not come up when the original "package" that led to RMS' resignation was published. It could be that new evidence has come to light since, or it could be that the allegation of transphobia is unfounded.
Some of the original allegations that I think are proven correct are that RMS:
- defended Marvin Minsky on a mailing list when Minsky was accused of sex with an underage woman, and made similar comments in defense of Cody Wilson. I believe Stallman's quote on the MIT listserv was that "[it is] normal for adults to be physically attracted to adolescents" when referring specifically to an allegation concerning someone under the legal age of consent. I think "sympathetic to paedophiles" is a defensible interpretation of such comments.
- The accusations of sexism are also supported by evidence, such as the "EMACS virgins" incident in July 2009 which RMS himself admitted the basic facts of (while claiming it was meant to have been a joke). One version of the lines involved reads "The virgin of emacs is any female who has not yet learned how to use emacs. And in the church of emacs we believe that taking her emacs virginity away is a blessed act." @daringfireball (John Gruber) also quotes a Wired article claiming RMS had a card on his door at MIT saying "Knight for Justice (Also: Hot Ladies)". I think "hostile to women" is a defensible interpretation of these facts, especially as there is testimony from women in tech who say they find this sort of thing hostile.