In my honest-to-goodness opinion, no.
Ray referred to the woman as she and her all throughout. He described her as great, with style, a great smile, zing, flair, pizazz and all that jazz! He DOESN’T say she’s deceptive or disgusting. If a man can’t handle male genitalia on a woman (especially those bigger than his), I don’t think that makes him transphobic. That’s just his preference.
Men aren’t OBLIGATED to be attracted to transgender women. As long as they treat them with respect and aren’t accusing them of being deceptive, disgusting or unnatural (which they aren’t), that should be enough. And if they don’t mind her genitalia or if they find it sexy, then good for them!
What Ray says in the song is very different from statements like, “It is a man in a dress” or “There are no chicks with dicks. Just guys with tits!” as in Ted 2.
What’s your opinion?
For those who haven’t seen it, here’s the video: