While I have never read the actual comic book storyline for "Civil War", I do have a "basic" understanding of the plot. For those not familiar with "Civil War", an attack takes place that results in the loss of many human lives, putting all of Marvel's superheroes in danger. The (American) government begins to lose it's trust in the latter, and consequently, a human registration act is passed, which encourages the superheroes to work as government agents. The Marvel superhero community becomes divided over its opinion of siding with the government, with the two parties being led by Iron Man (pro-registration) and Captain America (anti-registration), respectively. Marvel Studios has seemingly translated this storyline successfully into the context of the MCU: In the wake of Ultron's attack on Sokovia, the United Nations has passed as series of acts known as the Sokovia Accords, which would create a system of accountability over the superheroes. Iron Man and Cap, like the comic book, take their respective sides.
As a fan of Captain America in the MCU, I personally will be rooting for Cap in his efforts to counter the Sokovia Accords. Before I go any further, I will admit that government registration of the superheroes is understandable, considering Tony Stark's volatile and unstable nature. However, I believe that Cap's reasons are a little bit more justified. (It's Captain America, for goodness sake!)
Here's my reason: Cap is a superhero who represents the people's place in government. While he fights for his own beliefs and maintains a relatively strict moral code, his intentions are for guaranteeing the safety of the American people, as well as the world. After seeing what took place in "Winter Soldier", it's a little bit obvious why he would be objecting to government registration. He does not want to side with a government that has been secretly administering the growth of a terrorist organization that planned to wipe out the world population (HYDRA), and has also brainwashed his closest friend. If I saw that the government today was keeping information away from the people that the latter should know about, I would be livid.
And so, that's my reason for supporting Captain America in "Civil War", which comes out on May 6.