Sounds like she is an awesome friend, and that's what really matters. Romantic love really can come and go, whereas true friends are hard to come by. We like to this of this as a trans thing, but you're hardly the first guy to fall in love and have it be unrequited.
I really don't get the disapproval in this thread as though your friend doesn't think you are a "real" man. It doesn't sound like she has a problem with your transition or being a guy. She's just attracted to parts you don't have. Sucks, but that's reality. I don't begrudge anyone for being sexually into what they're into.
One other thing I'd point out is that perspectives change. One of my closest friends, whom I came out to first among my friends - is gay, and he totally supported my transition. He was immediately onboard with names and pronouns, even though it did not come natural. That was pretty evident when OTHER people would refer to me as "he" or "him" and I could see the second flicker before he recognized who they were talking about. Despite his acceptance of me, it wasn't for months until he felt like hanging out with me was like hanging out with a *guy* as opposed to just *me*, and now, he's referred to me as a man just by instinct, because it feels "right." What's changed is that I look and sound different to some extent, and the stuff we talk about has shifted ever so slightly.
People who know us the longest can take the longest to see us as different in any way, even if they "understand" what trans is and want to be supportive. It's not uncommon for her to have trouble really absorbing and internalizing you as a man, and that is the kind of thing that can take more time. It's definitely NOT the reason to ditch a true friend, as some people in this thread have suggested.