The big difference between Fury and the villains is that Fury is fighting for the status quo while the others are trying to fundamentally change America (and the world).
The movie is full of moral ambiguities. Nick Fury embodies these. He is on the right side but he is not above breaking rules. He has Cap's apartment bugged and has Cap under surveillance. When he discovers a ship owned by S.H.E.I.L.D. is involved in unknown activities, he hires mercenaries to take over the ship in order to give cover to the Black Widow who is ordered to make a backup copy of the ship's computers.
As an added bonus, we find that the senator from Iron Man 2 who was against private ownership of powerful weapons is on on the plot.
In the movie, data mining has been used to identify 20 million potential troublemakers based on such things as their credit history, their phone calls, and their library use. The plan is to use a fleet of three super-powerful hellicarriers to eliminate these troublemakers, thus bringing peace and control to the world.
The central plot in the movie concerns four controversies from the Obama administration - the increasing use of unmanned drones, the current policy of killing people who represent a general threat rather than ones who engaged in open hostilities, the unaccountability for drone strikes, and thebig diff use of data mining.
First I'll take the easy one - torture. While they do not waterboard anyone, Cap and company are not above throwing someone off of a tall building (and catching him on the way down) if it will save 20 million people. This is an easy one since they are trying to stop an actual event instead of discover plans for possible events. Cap's only concession is to delegate the dirty work to his sidekicks.
The comic book version of Captain America has often reflected liberal viewpoints. In contrast, the movie, Captain America/The Winter Soldier (CA/TWS) is one of the most conservative movie I've seen in years. Several parts of it show the logical conclusion to policies pursued by President Obama.I'm going to assume that anyone reading further has seen the movie or is unconcerned about spoilers.
This is a welcome change from the messages in movies such as Avatar (civilization is evil) and Noah (meat-eating capitalists deserve to die).