Most shops seem to be, though i found the more expensive stores to be the worst, or shops with a certain identity attached to them (like, Hollister, the beachy surfer dude look - it's always full of bros in their and i get what i want and leave asap because they're nasty sometimes). I find American Eagle amazing when i go to canada/usa, because the clothes fit well for one and the staff are always nice (and i've seen other trans people there). Same goes for many vintage/alternative shops, i've always been made to feel safe there.
One failsafe thing i've always done is to say i'm younger than i am if asked - i pass as younger but my voice is deep enough to not give me away as ftm, so i say i'm only 12 or 13 if someone is being really rude, or say i'm shopping for someone else.
If you're in the UK, primark is a big no-no for me. Judgement central, though in my local one they're sooo nice. I love river island, but the employees judge me hardcore there so i avoid them as much as possible (except for one guy who was really nice). Same goes for shops like abercrombie, department stores, the gap, and a few others. I used to love asian shops too, but i find they either love me there or they seem super eager to get me out.