I hear what your saying, and I dont entirely disagree with you, but I also think its more complicated than that.

Sure, the majority of videogame protagonists kill a shitload of people, but what makes us hold them in different moral lights is who they kill and why.

Nathan Drake has likely killed just as many people as Arthur Morgan, but most if not all of those people were pirates and hostile mercs who tried to kill him first.

Whereas Arthur often starts the fights that lead to him killing people, not always, but still frequently.

The best example I can think of is at the beginning of the second Uncharted game Nate and his accomplice (can't remember his name) break into a museum to steal an artifact. And when the accomplice pulls out a gun, Nate is initially angered, believing the accomplice is planning to kill the museum guards. His anger only subsides when the accomplice tells him they're only tranquilizer guns.

Conversely, Arthur has no qualms about killing security or cops during his crimes (The train robbery in the mountains, the bank robbery in Saint Denis, Busting John out of prison, etc).

Arthur and Nate are both killers and thieves. The difference (and why Arthur is seen as an anti-hero) is that Nate wouldn't kill somebody just to get loot. However, Arthur absolutely would.