I'm a big Captain America fan, and adored the 'Winter Soldier' storyline in the comics. The movie for the most part did a great job of incorporating that story to the big screen (As shown by the fact that the comic's writer, Ed Brubaker, gave the script his approval and had a cameo in the movie). I definitely saw it as more of an indictment of the paranoia and mistrust that the Obama administration has caused among fellow Americans than anything else. The fact that this revelation comes from the liberal publication Mother Jones must make it even more painful for the DUmmies. I loved the movie in general, and recommend it to all Cap fans.
SPOILERS!
Another thing to keep in mind about the movie is the sort- of subplot involving Senator Stern. For those unfamiliar with the Marvel movies, Stern is a liberal scumbag senator (His political party is never officially mentioned, but you can practically see the (D) next to his name) played by Garry Shandling. He had previously appeared in 'Iron Man 2,' in which he summons Tony Stark before a Senate hearing and demands that Tony hand over the Iron Man suit to the government, only to have Tony refuse and hilariously humiliate Stern on national television (The Senate hearing scene in that movie remains imo one of the funniest moments in the history of Marvel movies). Anyway, in 'Captain America: The Winter Soldier,' Senator Stern returns, and we learn that he is secretly a member of the terrorist group HYDRA, helping them slowly gain control over America. In the end, Stern is among those exposed when HYDRA's dirty little secrets are made public, and we last see him being confronted by FBI agents, so he'll almost certainly be looking at an indictment and tenure in prison rather than in the Senate.
I seriously doubt that a liberal- themed movie would have portrayed Stern that way.