Well technically a Protagonist just means problem solver, if we are going by Greek routes and it is still used for nearly any "good guy" no necessarily "main good" guy. We need to keep in mind that, main hero in the plot is not the same thing as main hero in the narrative.
As an example there is an episode of Justice League: Unlimited called The Greatest Story Never Told, where The Justice League are fighting Mordru, as this big epic end of the world fight, but the main plot of the episode is of Booster Gold trying to be a hero and stuck with minor busy work and a secondary end-the-world scenario that none of the rest of the League notice, let alone have time to stop. Now in that situation, The League are still the main-heroes of the plot, but the narrative has assigned that to a back-ground event while the main story in the audiance's point of view is following Booster Gold. Truth is as a trick of story-telling in that situation, and others like it the likes of Booster Gold are the Main Hero and Superman, Wonder Woman and Batman are the secondaries.