It feels like so many people just like it because of spooky stuff and not the actual message. This kind of stuff completely flies over the heads of anyone not invested in the genre. This is why it's so weird to me that it got so big.

The latter is the true game and directly criticizes the former. Basically, it's two games in one, the 'proper' DDLC and the 'creepypasta' version of it which is just Monika's (who exists in a layer above it) attempt to reprogram it. The true protagonists are you the player and Monika, with everyone else outside of the potential club president existing in their own fictional bubble. The protagonist is a total red herring and that's why Salvato wrote him the way he did.

By the time you're in the space room with her, his body is a hollowed out husk used as a vector for you the player to communicate with Monika. He's a piece of in-game code that only exists as a surface-level generic VN protagonist that's never held accountable because Monika fucked with the script too much and deleted all the character development because she sped up the bad endings (remember, she couldn't add stuff, only mess with the assets that were already there). The reason the protagonist never has an opportunity to learn anything is because he's not real.

Doki doki never ending tomorrow