Christopher Markus and Stephen McFeely, the writers for both Captain America movies as well as Thor 2, announced that the new Captain America movie will begin what is known in the Marvel Comic Universe as the Civil War. Adding to the already complex storyline featuring alien artifacts and invasions, the Civil War pits superhero against superhero as the government strains to reign in the rather destructive aftermath of superhero battles. This build up has been long coming and may have been seen as a minor point in previous movies. In the Iron Man franchise the US government sought to claim the technology developed by Stark and in the Captain America: Winter Soldier they attempted to use algorithms to predict and prevent future conflicts.
The Marvel universe is a rather exciting yet dangerous one. The first Avengers movie saw the destruction of New York on a scale that far surpasses the real world events of September 11, 2011. If the real actions of world governments following that terrorist attack are any guide then it should come as no surprise that they would seek to reign in the extra governmental actions of super heroes.
In the comic book universe Iron Man and Captain America were pitted against each other on the side of government registration and freedom, respectively. However the movie universe features a number of changes and will reconcile with the current cannon. Knowyourback.org is a great place to read what North American Spine has said about Captain America.