The Captain America in the movies isn't acting as honorably as the Captain America in the comics. In fact, his intentions are the least honorable, making him the real villain in Civil War.
It's the way they are wrote in y opinion
Stark comes off as a villain in the comics while in the film (in my opinion) he comes across as the one more in the right which is backed up by his actions in the past films and the effects of the consequences which weigh on him. Cap just comes off as arrogant and big headed thinking he's doing a noble thing because it's "his way".
Even at the end when Tony basically realises Cap was in the right about Zemo and comes along peacefully to work things out Cap ruins it by not telling Tony about Bucky's involvement with his parents death and gets in the way off Tony's rage. Now I'm not saying let Tony kill Bucky but at least allow the guy to vent when you personally kept it from him escalating the situation. Not to mention Cap in the film trying to make the point of "the safest hands are still our own" while watching videos of the Avengers destruction across the world while causing more destruction to prove a point.
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