Thing is, while I think you are perfectly within your right to have the pits of your choice, and indeed, to shave or no shave any other area of your body, I do think body hair shouldn't be on display on the commute.
I don't want to see body hair on men or woman in public.
You are right that men don't have the pressure to remove their body hair as woman do, however, aside from on the beach, mens normal clothing covers all areas of body hair. Few men in this weather are wearing shorts, and even then 'short shorts' haven't been in main stream fashion for men for a long time, and those who were sporting them this summer were also generally shaved/waxed.
Increasing numbers of men are waxing or shaving their chests, backs and arm pits.
Basically, if you don't feel the need to groom your armpits for display, why are you buying clothes like sleeveless tops to show them off? there are lots of clothing options for woman, sleeveless tops are an odd choice for someone who doesn't want to make a 'feature' of her armpits.
Plus it's strange to do a full on, theatrical, arms in the air stretch on public transport, I've never felt the need, perhaps the other woman was only looking at you oddly because you were doing this massive 'attention to my pits' style stretch? Unless it's like you've stuck a fake beard under each arm, she probably didn't notice them, unless you kept your arms up for a really long time to make sure she got a good old eye full.
Don't do attention seeking behaviour if you don't want attention.