Ya know, everybody keeps saying that
but this isn't Age of Ultron
Whedon was already working on an Ultron story, and they went with that title because they thought it was cool. No more No less. The comic story was brand new and far from iconic when the movie title was announced.
Civil War, on the other hand, is going to at least somewhat resemble the comics. There will be conflict between factions, public perception of heroes playing a large part, Cap and Stark coming to blows over a fundamental disagreement, issues of liberty vs security, and possibly even (if the rumors turn out to be tru) Spider-man caught in the middle of it all. Plus the fact that Civil War IS pretty iconic (even if a lot of people dislike it) and was one of Marvel's top-selling events, and this movie will be MUCH more similar to its namesake than Age of Ultron.
Winter Soldier is probably the closer comparison, where a good chunk of it is changed, but a lot of the characters at play, the themes, and even some specific moments are adapted almost directly.
Will it all be exactly the same as the comic? Not at all, but they're definitely calling it that for a reason beyond "it sounds cool"