This is one aspect of IM1 that always bugged me. I am ok with his identity being revealed eventually but I kinda wanted him to keep it secret for at least a couple movies. On the other hand, his whole bodyguard thing in the comics doesn't help much since even if nobody knows he's in the suit they all still know that Iron Man works for him. Peter Parker gets hunted down by villains just for being known as the guy who takes Spider-man's pictures. But Stark would actually get the blame for everything Iron Man does since he's his employer.
Still, having no secret ID does remove one of the more interesting aspects of Tony's dual nature: that being of how a lot of the public doesn't like him based on his history yet they all love Iron Man and the fact that they don't know they're the same person is an intriguing notion. The Extremis comic touched upon this. You have all the youth/lefty types out in front of Stark Industries protesting him since he's a defense contractor and the military is 'EVIL' in their eyes yet as soon as they see Iron Man flying away they cheer him. We can't explore any of that now without a reboot.