Hydra merch has been for sale long before this story with Steve Rogers though... and they've literally had Steve kick out Red Skull... I dunno it might be a shitty story but it's still a Hydra logo on a shirt, the same hyrda logo that's been on shirts forever.
Doing these things, for a some/a lot of people, isn't nearly enough to break that perception of Hydra = Nazi, though, especially when their film mediums (AoS and the MCU) have gone out of their way to highlight the Hydra/Nazi partnership.
And while Morrison may have tried to distance Hydra from the Nazis a while back before Spencer's run now, IIRC it was before/around the same time as when the first Cap movie came out as part of the MCU gaining huge prominence with the 'average' viewer, and (re)associated the two groups together.
The underlying problem here is that despite Marvel's attempt to 'safeguard' itself against Nazi sympathy claims by spending so much time making Steve explicitly NOT a Nazi (but still a fascist insofar as it relates to the style of rule), on some level, it's still using it for 'shock value' in order to try and sell comics, here.
Which is underscored in some examples we have seen of this Steve - while he's not explicitly racist against the Jewish population, for example, a flash-forward of the HYDRA future shows persecution towards mutants and inhumans.