What I usually hear is that the four writers for it all had completely different ideas on just who was “right” in the conflict. It was the ones in favor of the Anti-Registration side that portrayed Iron Man so badly in particular.
I swear I remember reading somewhere that Iron Man was actually supposed to be the one who was right, which makes sense since his position (at the onset of the series) was basically “maybe we should have prioritized mentorship and proper use of powers before we handed the guy who can just explode things a costume, a villain, and a reality show contract”. But apparently some people don’t want heroes who have to obey laws too, so the next thing you know he had a laundry list of misdeeds and an alternate dimension super prison.