Probably the only way to avoid being accused of whatever-phobia is to include no minorities at all! And that's probably worse!
I don't understand minority characters to never be depicted in bad lights or have bad things happen to them.
Well the idea is that once trans people are accepted as 'normal' rather than something special then we can treat them as we would a 'normal' character. Since we're not there yet then exceptions are made to present them in a more positive light than we would were the character a 'normal' white dude.
Personally I feel that 'normalising' minorities is best achieved by not making a fuss and simply treating everyone the same but as I've never been on the wrong side of any kind of prejudice then I tend to defer to those who know more about it than me. It's a question of accepting that we don't live in an ideal world and that until we do certain indulgences are going to be needed.
That's why we get white criminals and black judges on CSI, and why the notion of a straight pride parade is so ludicrous.