I don't mind the symbolic connections. Like the X-men/civil rights connection etc. But I've always hated the more direct connections. Maybe that's why I'm not a big fan of Captain America. As far as Captain America #1 goes... I assume you mean the original issue from 1941? Back then I think we only had Captain America, Namor and the original Human Torch... so it wasn't the shared Marvel Universe like we have now. I assume the Captain America stories were fairly self-contained.
The Marvel Universe now is a ridiculous fantastical place. With reality warpers, people raised from the dead... it's hard enough for me to buy into the universe in its own terms... but bringing the real world politics directly into it just makes it fall apart for me.