I think the point is that the only guy who we could possibly want to like is so totally unlikeable. I don't think "flagship character" means we should like him, and I don't know that he's everyone's favorite. We're not there just yet, but it becomes evident later that he's the only one we could possibly side with, and he's fucking mental. So what does that make us? Thick? Insane? Simplistic? Someone is definitely accusing us of being wrong in our thinking.
One of the trickiest things to learn in writing is Point of View. The more POVs you have, the more story you get to tell... but the fewer POVs you have, the more pure and relatable your tale. Watchmen has shit tons of POV. Without spoiling too much for the next couple weeks, it's worth noting who has POV and who doesn't. That said, each character is a protagonist of their own story, really. Some are more relatable than others. Nite Owl, if anything, is the story's access character - he was a little boy that loved superheroes so he became one and it wasn't all it was cracked up to be. Laurie had no choice but to become a superhero and she hates it through and through. I'd say she has just as much POV as Dan does. More than Rorschach.