Doom is important. Doom protagonist isn't. Minecraft is important. Minecraft protagonist isn't.
For one thing, there'd be no game if you didn't have the lead character you play as. That alone is very significant.
Admittedly, I can't speak for Chief's character as I haven't played a Halo game before, but if you go by this logic, characters like Mario, Link and Samus wouldn't be in Smash at all either. Come to think of it, we probably wouldn't
have Smash Bros. to begin with if this logic was applied. The only characters in the first entry in the series who
weren't the playable lead protagonists of their own respective franchises were Pikachu and Jigglypuff, who are still icons in their own right (Jigglypuff more so at the time of Smash 64's release, IIRC the anime heavily influenced the decision to include her). The whole series started with a crossover showdown between the icons of Nintendo games, most of whom were the main, playable characters of their franchises.
It goes without saying that gameplay is integral to every video game, and what the playable characters can do is usually a pretty big part of that gameplay. Mario's got his athletic abilities and powers up, and SM64 later showed him to be a fairly good physical fighter, Link's got his assortment of items along with his sword, and Samus has her numerous advanced weapons that come with her power suit, including her arm cannon. They all also went on to become the faces of their respective franchises from then on out. Master Chief is in the same boat as them in those regards.
With Doom Guy and Steve, I can kinda see where you're coming from as I know they don't exactly have defined identities, but they're still the playable characters of their games and have, like the others, become icons of their franchises. Even if most players in Minecraft opt to use custom skins, Steve is still the original default skin that remains one of the two defaults today, appears frequently in merchandise (he's featured prominently on the covers of console editions of the game) and I think it's safe to say that you'd have a hard time finding Minecraft players who don't know who Steve is.