Betrayal...Simple as that.  Yes, he thought he was doing the right thing, but so did Judas when he betrayed Jesus...
 
Consider these two panels from Amazing Spider-Man 535... Peter demands to see prison 42... Please note that I added them in reverse order so read the bottom one first... We see that Stark not only KNOWS what he's doing is illegal, he doesn't care...  He KNOWS he's violating civil rights...He KNOWS he's operating outsides the boundary of the law...and he's basically saying it would be bad for anyone, even friends, who stood against him...  He basically stated that he would do whatever he wanted, to whomever he wanted, their rights be damned.... 
Now, when Peter decided to leave resign as Stark's second in comand, and leave Stark Tower, what exactly does Stark CHARGE him with?  He  had broken NO laws...  He HAD registered.  He had done absolutely NOTHING illegal, but Stark attacked him and ordered his arrest... He never once mentioned what the charge was...  How is that not a betrayal?
 
Stark had no legal grounds to take away She-Hulk's power but he did...Only minutes after having sex with her; talk about adding insult to injury...  He SAID he took away her powers because she stood against him...  How is that not a betrayal...
He used Thor's DNA, without Thor's knowledge or consent, and cloned him into a killer cyborg... betrayal...
He ordered mutants onto a reservation (xavier's estate) and surrounded them with Sentinels.  He ordered that they be injected with microchips so they could be tracked... Betrayal....
He forced Cloud 9 to register and join the initiative even though she was only 15 and the registration act did not apply to children... He said, "Laws change..."  Implying that the law would eventually be changed to include children but it DID NOT include them at the time, so it did NOT apply to her... He had no authority or legal grounds to incarcerate her... BETRAYAL to anyone he believes in the rule of law...
The list goes on and on but the point is made...

The thing for me, Iron Man was my favorite superhero until he revealed his secret identity (I'm a comic book purist, heroes should have double lives, just a personal preference) but even then I still did like him. When Civil War happened I absolutely understood why he'd be chosen as the leader of the the Pro-registration faction - it makes sense for him to be, but I found him so unlikeable and still have since, I mean after Civil War my opinion of Iron Man was pretty bad. An I still don't like him as a character anymore; the movies don't help either (nothing against them they're great) you know in the movies Tony goes through this big life changing event, then by the end he goes back to being a prick (and he reveals his secret identity at the end). That's kind of how I see Tony now, at one point he was a good likable character but progressively the writers just make Tony do more and more unlikable things. Such as the retcon/tidbit about how he combed the couch of the Avengers Mansion for Thor's hair after the first meeting of the Avengers which was something that I just hated. But I mostly blame that on Mark Millar and his overly cynical characterizations; just look at the Ultimates. Or how he became the head SHIELD and felt really out of place, the Initiative thing (which I really despise) and now it would take a major change to bring me back on board with Iron Man.
 
But in terms of his actions in Civil War, yeah he betrayed them. Absolutely. Such as the whole Thor hair to make clone thing, that's a betrayal. Putting his former friends in the Negative Zone prison. Iron Fist, as Daredevil, even calls him Judas and I'm inclined to agree. Because the SHRA was a horrible idea; the idea of a superhero civil war is great but bringing the whole registration act was awful, I've never been big on bringing those kind of issues into comics especially when it involves the government essentially press-ganging superheroes into working for SHIELD, which doesn't even belong to the government it belongs to the UN, unless they changed that. Because superheroes aren't above the law, they should work with the law certainly but not for the law. That just makes it a job which superheroics shouldn't be and it isn't; if anything it's a really extreme hobby. Heroes shouldn't want to be paid or get vacation time; seeing as how they should have an alter ego...with a job and it's own vacation time.
 
Anyway that's my overtly long answer to saying Iron Man is a jerk and the SHRA was crap.

@VenomX10 said:

@FadeToBlackBolt said:

Tony turned into a dictatorial douchebag during that event.  I still haven't been able to like Iron Man since Civil War. Because of the SHRA, Aunt May was shot. That's a really good way to protect the innocent.   ANTI-REG ALL THE WAY.

Proof that the SHRA wasnt a good idea, Aunt May got shot because the government mad Spider-Man reveal that he was Peter Parker, meaning that all his villains could find his loved ones and use that against him. The same goes for all the heros with secret identities.  Even if the government did require all, "Costumed" Heroes to register, would they there fore be hypcritical, because they mask the Idenity of many of their own, including CIA operatives and Special Forces, soldiers, etc. etc. and finally....ANTI-REG

So the loved ones of the heroes are more important than civilian lives, who are at risk of more incidents like Stamford?

1. The one thing i've never understood was how the SHRA would prevent something like Stamford from happening again cause if i'm not mistaken, since the CW there has been how many extremely destructive superhuman catastrophes, the final CW battle eventually almost being another if cap had not realised the damage they were causing.
2. The one single event that proves that the SHRA was ill planned was the secret wars and the ascention of norman osborn (arguably the joker of the marvel universe) into a positioin of absolute power enabled by the SHRA which would give him access to all sensitive information on any superhero he wanted.


@cody1984: 

However, the government building robots to deal with mutants who could level cities is completely justifiable.