Based purely on a character front, the fact that this story has generated the kind of "controversy" that it has does seem a little bit surprising as Superman has long seen himself as a servant to humanity rather than a tool of the U.S. government (Frank Miller's The Dark Knight Returns not withstanding). That's the important thing to bear in mind: in the Action Comics #900 story by David Goyer, Superman was NOT somehow denouncing this country as so many people have construed, but, instead, is emphasizing that his role as hero is global.
In some ways, the character said it best himself in the one highlight from Superman IV: The Quest For Peace, when he addressed the United Nations.