Hi Brianna,
I am also MTF and I have faced the same issue. I am pre-op and I didn't start HRT until literally today, but I have been using female bathrooms for the past couple years when I am running around as my preferred gender (that was rare two years ago, fairly frequent now but I am not full time). I am hoping to be more presentable several months or a year from now as HRT kicks in, and with FFS in the future, but I can't hold off and not pee until then...
I have never encountered any hostility or problems in any bathroom - ever. Earlier on I discovered my fears were my own, as if the earth would stop turning if I did something wrong (and what I was doing wasn't even slightly wrong). What works for me is to show self-confidence even if I don't have it at that particular moment. Act like you are supposed to be there and you won't get questioned.
I'll admit the first time I used the women's restroom I felt like the entire planet was going to stare and point. I was so relieved it was empty. (The restroom, not the planet). Took about a half dozen times to get even slightly confident about it. At the other extreme, I was at Ikea the other day and the women's restroom there is like a chat room or social club. I am gradually learning women's restrooms are a handy place to adjust makeup, people do that all the time.
I am very sorry to hear you had such a bad experience on this topic when you were younger. There is no excuse for physical abuse but the past cannot be changed. I hope you also have some good memories from that age. That is probably causing you even worse fears than the ones I had to overcome. I don't know if you are seeing a counselor or therapist, but if you are I would suggest you bring this up with them. Either way, please know you are not alone in this.
Kendra