Civil war is coming. Prepare yourselves. In 2016, Civil War will erupt with fury.
In Civil War, the governments of the world will unite and pass an Act that would require anyone with superhuman powers to register. This would be done so the governments could regulate superhuman powers. The governments see the super humans as a threat and consider them walking WMDs.
However, Civil War may have been teased as early as Iron Man 2.
Remember the scene where Tony Stark is constructing the Particle Accelerator and Agent Coulson picks up Captain America's shield? Tony just blatantly didn't even acknowledge the shield and continued on his own work, using the shield to level the accelerator. This could be the first inkling of Civil War, we can see that Iron Man, didn't really care to know about what the shield was about, because he was too busy working on something for himself. This is the first step in setting tension.
By setting this event, it already would create a little tension between Iron Man and Captain America, even before The First Avenger was released.
The second instance of tension between Iron Man and Captain America was during The Avengers, it could be seen that Iron Man and Captain America were working on different frequencies. They even quarreled a tease on the SHIELD Helicarrier when Tony was trying to provoke a response from Bruce Banner.
Then a clip was leaked of the Avengers apparently during some down time chopping wood and Iron Man and Captain America go at it again.
All these events are leading up to Captain America: Civil War and Age of Ultron will bring these two to the realization they can not be together and thus creating a separation between the Pro-Registration and Anti-Registration.