I guess I'm kind of in the other camp on this. For one thing art, even as silly as superhero movies, should help us deal with reality, so BECAUSE there are so many who would think Nazi characters were the good guys is exactly the reason why they need to be more present again AS THE BAD GUYS.
People need a reminder that Nazis are the bad guys, have always been the bad guys, and always will be the bad guys.
See that quote in my signature? Gustave Gilbert was a psychologist, and he came to this conclusion after analysing the accused at the Nuremberg trials. His definition of Evil came from studying Nazis and their motives. Because being Nazi means being evil, and if a Nazi does not want to be evil anymore, if they want to reclaim their humanity, that process, with whatever other steps are needed, also always entails stopping being a Nazi.
Too many people seem to have forgotten that, so we really need to drill it back into public consciousness. Nazis are always the bad guys, because Nazis are irrefutably evil.
So, yes, have a Nazi Captain America, because that would be a great bad guy. Because Evil, just as Nazis, can come around looking like people we previously held in high regard. The reason why Alexander Pierce was a great bad guy is because he looked like the late Robert Redford. We, the audience, think of Robert Redford as a good guy, but then Pierce went and had his housekeeper killed and schemed to kill our heroes and thousands of others while putting the whole world under his control. A person with a face we trust goes and does undeniably evil things.
So, yeah, I'm all for stories like that which teach us to be vigilant, and that Nazis are evil and need to be opposed.