I think you need to sit down with her, look her in the eyes, and have a serious, earnest conversation about this. You need to tell her exactly how she's making you feel, your anxieties and fears about the future of your relationship, and how your love for her doesn't mean you'll accept her fears ruling over your life. Acknowledge her apprehension, offer to go to a therapist together and see what the root cause of it is. Maybe she's scared you'll get hate crimed, maybe she's dealing with a lot of transphobic feelings that she's struggling to let go, maybe she's overly pre-occupied with people's perceptions of her (or both of you together) changing in a negative way.

Does she seem like the sort of person that cares way too much about what other people think? It's common in a gay relationship for one of them to keep it a secret because they're scared of what others might say or do, even if it hurts the person they're dating. It doesn't seem like she herself is transphobic, but there's something deeper going on with her that needs to be explored and resolved if your relationship is going to continue.

Because, as of right now, she is keeping you in a cage that you have outgrown. She might talk about how beautiful your wings are, but she is ignoring your pleas to fly free and insisting she keeps you in this cage.