I really like how they drove that point in winter soldier and a bit in avengers 1 . By the first avengers movie even Nick was probably getting suspicious when they ordered the nuke strike on new york. This dialogue between him and cap was good
Nick Fury: After New York, I convinced the World Security Council we needed a quantum surge in threat analysis. For once we're way ahead of the curve.
Steve Rogers: By holding a gun at everyone on Earth and calling it protection.
Nick Fury: You know, I read those SSR files. Greatest generation? You guys did some nasty stuff.
Steve Rogers: Yeah, we compromised. Sometimes in ways that made us not sleep so well. But we did it so the people could be free. This isn't freedom, this is fear.
Cap was right...