Like I said, in the comics, Cap has to adjust to a system that he has to distrust moreso than he believed was the case back in the '40s. But his ideals remain intact. You can have ideals about the country (liberty, justice, inalienable rights, protection from exploitation and hysteria, etc.), while treating the system entrusted with protecting them with heavy skepticism. In that sense, what you see in Avengers, and may very likely see in the new film regarding SHIELD and the government doing shady things are allowed to happen. Cap will learn from them. But he keeps his values intact. His value =/= trust in government. This is a very clear subtext in the comics, from the '70s until the more modern comics with Civil War and the aftermath of it. If he lost his values and ideals, then as jye suggests, he wouldn't be Cap anymore. He might not become the Punisher, but he may be more like Iron Man in the modern comics, or US Agent, or various other characters that may lose sight of what Cap sees as the real U.S. values that he represents and is tasked with protecting. Cap is not a sheep, following orders without question. He sees it as his responsibility to do what he feels is right, in order to secure and reinforce the U.S.'s fundamental ideals. You might miss this if you never read or didn't understand the comics though, so I'll give you a pass this time.
