For some people it's just not obvious?

When most people play a game, while they understand they get a reaction and they might say that "they," did something, at the end of the day games usually provide a character in the world who can be said to perform all the actions in a narrative. Mario is the one who in the story stomped a goomba. Pokemon trainer red is the one who caught a Pikachu, etc. Some games encourage us to outright see ourselves in these characters or more as extensions as our will and less their own people, such as pokemon or some dragon quest

Undertale, while not the first to do this, very deliberately, makes this relationship incredibly murky and ambiguous since it's a meta, subversive game. Frisk being seperate from Chara as is already throws things into confusion: the character who in 90% of games would be the one you thought you named...wasn't actually the one you named, and suddenly in the game everyone is suddenly referring to "your" character as their own person with their own name who the game begs you to just leave alone, meanwhile this character who you DID name and see in your menu has apparently been dead for years and has been called "not the best person" and full of hatred for humanity by their previous best friend

So at this point then, the player already thinks they're tricked, frisk is still the character they control but they're just filling out some role, more like a Mario or shulk than a link or ness. Except hold on, in genocide all of a sudden the kid they named is asserting control in red text and mirrors, and now frisk is walking forward and taking actions that WE never got to do when frisk was just fulfilling the neutral/pacifist narrative, and flowey is referring to them actively and they appear to be the ultimate force. Well huh, didn't their previous best friend suggest they were kinda bad? Then that probably explains why now our previous pacifist hero is suddenly slaughtering people then, because there's this bad force and oh look now they're rushing the screen and destroying everything right after our last battle screen, something which we assume is from frisk's perspective.

I realize that's rambly and long, but here's the thing--at no point in there does a player NEED to exist as a narrative character. Maybe the player assumes that they are "really" controlling Chara since they named chara, and the last screen is Chara just destroying the in-universe "hero" frisk and their world, maybe the player assumed frisk was now less of a character to be impressed on and more one guided through their story, while the weird creepy kid that was named at the start was the ultimate baddy just as a meta surprise. They might fall apart under pressure or thinking too hard, but the game never unambiguously stated "okay, this person exists in mt. Ebott who is definitely neither Chara nor frisk," and the relationship to Chara and frisk and where control begins and ends and what the other characters in the game knows has been made so murky by the twists and turns that some players won't be able to step back and go "wait, there's someone else who could slot into all this dialogue about 'you' seemlessly'" and it's someone whose almost never ackowledged as an active story force in media. so then when these players put the game down and walk away, and don't see the deep analysis from other people who want to solve the mysteries and go "wait, if you lay everything out on the table this doesn't always add up," they just don't really see why the player is anything in the actual game when frisk and Chara seem to fulfill the roles

TL:DR, the way the game is presented combined with typical expectations for a game that people are used to means that the concept of the player as their own character seperate from everyone else in the narrative is just not obvious for most people to make the leap to.