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