I've been studying what I think is the historical origin for transphobia and I think the best answer I can give is it was an accident through monotheism post Egyptian rule. The ancient world had a niche in which temples formed and practiced a necessary action within society that you catch-all church won't do. Like transitions for example.
The ancient world was not a stranger to trans people, even if it didn't always know how to handle them. Trans women were generally regarded as strange men, and Trans Men were as mad women. But their temples existed and it was if not widely known, certainly widely practiced methods of estrogen and testosterone extraction, Bottom surgery, and top surgery. And they were exempt from laws forbidding those practices in a cis environment. There were pride parades, and even amazingly, drag bingo, club nights and crossdressing parties.
These didn't go away, we've always been practicing these even if we are missing the crucial education of that time. There's always been trannies making hospitals somewhere.
When you begin to unearth the historical data yourself it's actually staggering to see the enormity of what trans people have contributed frankly, to all expressions of art, creativity and communication. There's been times when that's been widely known and celebrated.
I can't argue that we always had a fair place in society, certainly the furthest back trans people I can guess at are likely doing highly dangerous work like charioteering, potentially for our tenuous place in that society, I cannot say without studying more.
This is the truth as I see it, as I can argue for. I pray to have the ability to educate this to the world, that there is no reason to hurt us and every reason to restore us to equal members of society. For society's chosen, pain is treated, injury is repaired, suffering is eased. If you understood the enormity of this injustice, it's my belief you would come to the same conclusions we have about our own safety, health and happiness.
Please always ask questions of your world