The debate revolving around the big question continues between fans of the MCU and Marvel Universe fans.
Who's Side Are You On?
To completely answer this question honestly, I've decided to take a look at both sides. Here's how Wikipedia explains the civil war.
Civil War follows the implementation and consequences of the Superhuman Registration Act, a legislative bill which required the mandatory registration of any person based in the United States with super powers. The act arose due to public pressure for accountability following a series of superhuman-related events causing significant damage and death within the Marvel universe, such as an attack on Manhattan in reprisal for Nick Fury's "Secret War", and the Hulk's rampage in Las Vegas which resulted in the death of 26 people. When the mutant population was drastically reduced in the aftermath of M-Day, itself caused by a mutant, anti-mutant hysteria caused by extremist groups caused a majority of the remaining mutants, known as the 198, to relocate to the Xavier Institute, and raised public support for the proposed act.
Public sentiment toward superheroes plummeted after an incident in Stamford, Connecticut, in which the New Warriors, a group of young superheroes and the focus of a reality TV show, botched an attempt to apprehend a group of supervillains in a quest for better ratings. In the resulting fight the villain Nitro used his explosive powers to destroy several city blocks, including an elementary school at the epicenter, resulting in the death of over 600 civilians, 60 of whom were children, with just Speedball of the Warriors and Nitro himself surviving. Although many high-profile superheroes assisted in the relief and rescue effort, there were a number of isolated revenge attacks, and support for registration rose.
The prospect of registration divided the superhuman community down the middle, with Tony Stark, the superhero Iron Man who had previously tried to halt the act, becoming the pro-registration figurehead, and Captain America leading the anti-registration group. Iron Man, with Mr. Fantastic and Henry Pym, argued that the changing political landscape meant that resisting the law was pointless, and that it is reasonable for heroes to have proper training and oversight, whereas Captain America, alongside Luke Cage and Falcon argued that heroes required secrecy in order to protect aspects of their 'normal' life, such as spouses and children, and to allow them to act in whatever means necessary against threats which the ordinary emergency services couldn't cope with. Although nominally a U.N. agency, S.H.I.E.L.D. assumed the brunt of enforcing the act under acting director Maria Hill.
Anti-Registration (Captain America's Team)
Captain America has very persuasive and purposeful reasons as to why he is leading the anti-registration group. Basically, everyone on the anti-registration team wants to keep their identity, so that their families aren't persecuted or targeted by most villains, to be used as weaknesses. Also, most of the heroes on this team are humble, and don't want to be recognized for their duties. But let's face it, its mostly the first reason. Am I right? Now that's a pretty damn good reason.
Pro-Registration (Iron Man's Team)
Iron Man also has a lot of good reasons as to why he's the head of the pro-registration group. These reasons are actually very reasonable. First off, everyone with powers/abilities would be kept track of, and any crimes committed by these people could be addressed properly, instead of the government not knowing what to do when an extremely powerful being terrorizes a part of the USA, or even the world. Plus, people who want to use their power for good can receive proper training to become a hero to help protect people as well.
Both these teams have really great reasons as to what they feel about the Superhuman Registration Act, but I'm going to have to go with the Anti-Registration group. Let's face it, it's all a matter of opinion. Some people want it one way, while others want it the other way.