Captain America was wrong.If it was just registering then it would not be a problem but Stark's registration basically meant you were entered into indentured servitude to the government. And saying no got you shipped off to some prison in another dimension.
You had people who had been working side by side with Stark now being hunted by deputized super-villains all with the co-sign of Iron Man which didn't help the situation either.
Stark was a shytheel for everything he did with the SHRA.
And he's an idiot
If you're going to be a soldier you have to be in a military.
If you want to be a super hero fighting crime, in events that lead to the destruction of cities and destroy lives you can't be out there rogue.
If you have powers and want to work at McDonalds you don't need to register. It's simple