No, I think they're so secure in their gender/sex that they can't imagine that others don't feel connected to their bio sex, and that that's why they don't think being trans can be a real thing. I think it's somewhat similar to why religious people can't accept the atheist view that god doesn't exist and vice versa, for example. Two different world views clashing.
I only really come across transphobes online though. In real life, they either don't live anywhere near me, don't know I'm trans or keep it to themselves. Where I live people either just shrug about it or are kindly curious. Me passing always, probably helps keeping any potential transphobes away as well, cause I appear like a cis guy.
Only once I was harrassed irl for being trans, when I still didn't pass and lived elsewhere, 7 years ago. It was more annoying than scary though. The guy was rude, obnoxious and wouldn't stop asking me about my gender in a very heckling way while laughing at me, but he didn't seem dangerous. He seemed more scared than I was. He reminded me of my childhood bullies who were loud but got frightened when I fought back. I can't pretend to know what was his motive, but I think he just saw an opportunity. Wasn't the best of neighbourhoods to live in, lots of iffy people, robberies and other crimes going on.