Having grown up around a lot of gay and working closely with a number of trans people, I have come to the conclusion (possibly wrongly), that they will forgive a lot of "-phobic" speech, as long as you accept the criticism they provide.
One of the critiques I often got was to be more gender inclusive in my speaking. Which a lot of people do now (re: replacing he/she with they). From what I read, it seemed like this person would provide feedback that would either be ignored or the contributor/employee/whomever would actively retaliate against.
It really isn't how you mean something, it is how you make someone feel. If you are trying to run an inclusive community, that distinction is very important.
All of the "accidental racism" of years past have now become "accidental -phobic".