Iron Man came across a villain in the comics, Civil War. I loved Iron Man, always have, alot more than Captain America, but I found it really hard to side with him during that event. Even in the aftermath Iron Man came across as a horrible horrible human being.
Captain Marvel (then Ms Marvel), came across really nasty too and she's my favorite female Marvel character lol. The fight between Captain Marvel and Julia Carpenter (one of the earlier Spiderwomen) hit me quite hard when Carol literally tore Julia away from, her daughter because she didn't sign to the registration, then convinced herself she was doing the right thing...
Took me a while to get back into the Iron Man and the Captain Marvel characters again after that but I did garner new love for Captain America though...