This is a really difficult point, and I'd like to address it anecdotally .. in part because I have no actual data to share anyway, but also to put what I'll go on to say about transphobia in some perspective.
My first sexual encounter with a trans woman was with someone called Jamie (not her real name even at the time as it turned out, but how she first introduced herself to me) who I met at Heaven in 1995 and who I spent a rather torrid couple of weeks with before losing touch completely, in the way of things back then. She did have a penis, and that didn't bother me at all (quite the opposite actually). Anyway, I never saw and have never seen Jamie as anything other than a woman - despite the penis she was every bit as feminine as any woman I've met, as contradictory as that may sound - and she exists in a nice part of my mind where good, positive, even vaguely loving sex-memories reside. But I feel most of the straight-cis men I know would not even consider a dalliance like that, and I'm certain most lesbians wouldn't consider it. Would this be transphobic as such, or would the phobia / distaste centre more specifically on the presence of a penis? I can't answer for other people, but I suspect the penis itself would be an issue over and above Jamie's dirty laugh and beautiful eyes and cute breasts and other alluring aspects.
On the other hand (and still anecdotally), I should mention someone I met more recently than that, though still quite a few years ago now. Her name was P* and she was a fully-transitioned trans woman. We met in a pub in Bristol (long before I actually moved to Bristol though) and things began with her drunkenly ranting at me about all the abuse she'd suffered and was still suffering. I listened, we talked and ended up laughing, and went to a couple of different pubs where we did certainly attract some weird and unwelcome attention. It was scary.
During the course of all this she mentioned her expensive new vagina (her exact words) and the thing is, at that point any fancying I felt for her just evaporated. It was really awkward, and to cut a long story short the night ended with me being yelled at and slapped for being transphobic. Essentially, the idea of a surgically-created vagina really freaked me out. I mean, I was drunk by that point, OK, but the idea of (to me) missing bits and a cosmetic job in their place just .. well I can't put it better, it freaked me out. I think it still does and I have to be honest, if I ever got into something with an attractive trans woman again I'd still rather she had the intact (male) bits if I were to get into a sex situation.
Maybe it has something to do with orgasms, wetness, clitoris, G-spot, I don't know. The person is a whole person - I get that. But for me, something is wrong. So, I believe this is a kind of transphobia, probably .. and though I am vaguely uncomfortable at having to admit that, I have to. It doesn't change how I ally myself with my trans- brothers / etc / sisters in their struggle for social acceptance. And it doesn't have anything to do with their image of themselves as being physically right, which is more important than what anyone else thinks anyway.
I would add that I've never had sex (or even a snog tbf) with a trans man, though over the years I have met a few guys who are trans. Again though, I instinctively feel that if sex happened with a trans man, I'd end up more interested in the vagina (that was natural) more than the penis (which wasn't) and I'm aware of how hurtful that would be. Hence it's not something I've ever sought out.
Again though, this has little to do with a whole person who needs love and acceptance, and I apologise if anything I've written here is hurtful or upsetting to any trans person who reads. It's an honest perspective, is all I can say, and I don't consider myself a transphobe.
I have to add a last point though, about this being all about sex. I think trying to take sex out of it completely is misguided, after all, we are talking about sex, gender, sexuality, genital preferences (on self and others) and sex behaviour. But something I remember P* talking about at some length is how men were happy to fuck her, but finding anyone to hold hands and snog openly with during a night on the town was way more difficult. I think this is the phobia in action too (she certainly did) and I also think it's a far more subtle and (dare I say) harmful expression of it.
So yeah, Too much information. But the main point is this: I do think more of us are more transphobic than we would really like to admit, even to ourselves. I certainly don't think everyone with transphobic feelings feels ashamed of them or even feels they should feel ashamed of them - though I do think some people with transphobic feelings would deny all that anyway, even to themselves. It's not transphobia, it's...
However, I think rather than shaming ourselves and each other over it we could all just do with a bit more honest self-reflection. There's nothing shameful IMO, in finding trans-ness weird and hard to deal with. There's nothing bad about feeling uncomfortable with people seriously challenging something we consider basic, settled and take for granted - in a way, it's all a part of getting older in a world that never stops evolving. But what we do with those feelings matters - whether we retreat into preconceptions and put up walls and attack, or if we try and engage positively with something that isn't going away any time soon.
