On the one hand, Cap has been betrayed, as it were, by the system. Hydra essentially took over SHIELD, leaving Cap with the feeling that the system was corrupt.
On the other hand, who watches the watchers?
Actually, this can be equated with Skybreaker vs. Windrunner. Not as far as powersets go by any means, but ideologically. Iron Man wants to follow the law, while Cap wants to protect his friend, someone who cannot protect himself, as it were.
And don't tell me that Bucky can defend himself. I know he can, but against the might of SHIELD he would probably loose. Cap would as well. But team up, they can dominate.