Two things:
- Nakamura, while often considered the world's best living blitz/bullet player, hasn't spent equal energy on his classical game. Carlsen spends far more energy training for classical chess.
- Style differences matter. Carlsen is a "grind it out" positional player, Nakamura is a tactical monster. The latter works well in speed chess, but the former prevails in classical.
Nakamura does seem to be able to get good positions against Carlsen and good positions which suit his aggressive style. But a point seems to come when Carlsen's stout defending tilts the balance of the game and once Carlsen has the edge it is pretty soon all over.
Maybe Nakamura needs to be able to concentrate intensely for just that little bit longer, or find just that little bit more intuitive feel for the attacking positions he creates.
Anyway I hope he stays true to his attacking instincts and does not start to put safety first Azeri style. Better to lose playing fighting chess than that.