So, on the whole, Civil War seemed to actively demonize the pro-reg side. They made incredibly stupid and often evil decisions like hiring teams of super-villains. Based on the last few years, that level of incompetance is realistic, but not for the chracters in question. Anyhow, so given all that, how come they won? Is Marvel saying that they're right?
Hell no. I'd bet money that this is a precursor to the anti-reggers finding ways to subvert the system. Probably Reed will flip sides at some dramatic point, possibly revealing this as his plan all along (he's still acting OOC from what I've heard, even if this was the case). We're probably also just going to see the thing fall apart in a myriad of seperate stories.
In short, think of the end of civil war as the 2004 election. The second arc is the story leading up to the 2006 election.
This is why I'm potentially okay with the death of Captain America if they do the follow-up well. It's basically how I felt in November of 2004.
Anyways, this doesn't mean I approve of Civil War on the whole. Nic has an excellent argument that the premise is just bad for story-telling in the universe. The whole government sponsored teams things disrupts a lot of books while at the same time being fairly irrelevant to the lives of the readers. It doesn't quite manage to be topical or interesting. So I actually can see the story they're telling, they just should have done it in a standalone miniseries or they should have found a different premise that would let people act IC.