It was Chugga (one of the other guys from ProtonJon's LP group TheRunawayGuys) who had the false allegations made against him, and while Jon didn't throw him under the bus completely, his "support" was flimsy at best and he was clearly prioritising his own optics over Chugga's wellbeing. When you look at how Tim/NintendoCapriSun (the third guy in the group) was going above and beyond to look after Chugga when he was suicidal from it, going out of his way to clear up misinformation and misunderstandings about what had happened, and generally keeping his fans in the loop about how he was doing, it became very obvious who was the real friend and who was the business acquaintance.
They seem to have made up since then and I get standing by someone who's been accused of paedo shit is obviously harder than the usual "he did a heckin' racism" callouts (even if you know for a fact the allegations aren't representative of what actually happened; you're gonna eat shit for it no matter what), but consistently playing it safe rather than going to bat for his "friend" of over a decade really soured me on Jon overall. I obviously can't know for sure if he actually has gender dysphoria or if he's just let the Internet convince him he's trans, but given he's let the Internet sway his opinions on serious matters before, I'm not all that convinced he's thought it through properly.