It's all what you're desensitized to in media. We have all sorts of tiers of violence, but we don't handle emotions and interactions the same way.
Popular games thrive on conflict and action, generally in the form of violence. We don't see any agenda in it because it is omnipresent. People can deconstruct it afterward, but we don't say, "The character stabbed the enemy in the right eye, that is a commentary on Austrian economic systems".
Maybe Naughty Dog is presenting a view of the world, maybe they do see themselves as a propaganda arm in social engineering. I doubt it. I think they want to explore subject matters and have a differing worldview to many as would be expected given the number of views that exist.
Romance exists, homosexuality exists, you are free to not support it, but I think taking showing something and making that out to mean indoctrination is a leap I don't see.
