Dan Salvato himself answered this question on Reddit.

He confirmed that the protagonist is only meant to be an avatar; a vehicle for the plot to occur, which is why he kind of stops reacting to the world around him when things get weird, and why he just basically disappears by the end of everything.

The male protagonist in-game is literally the least important character in the entire game, and was made simple and sort of unlikable on purpose, as Dan was aiming to make a generic VN protagonist for who the girls fall in love with for no good reason other than it being how the game is programmed, just like in actual VN games.

The source on the right takes you to the DDLC subreddit. Dan has an AMA thread there, which you can easily find by sorting threads by score. His reply must be somewhere inside it.

Just my thoughts on the matter, but: