Eh, I didn't think the movie was that good but I did enjoy them portraying Superman as more of a single individual instead of the magical savior that always seemed to save everyone from doom.
One last thing; it seemed like the story was more focused on Krypton anyways. Superman himself was certainly the sideplot in the movie.
It was pretty obvious once the world builder machine started that Superman was still just one man. Even he is not enough to save everyone from death. He simply can't be everywhere at once and when fighting super beings like himself, he's not going to be able to avoid collateral damage and casualties. (Although one could argue that in all the destruction he causes flying through buildings and such, you don't actually SEE anyone die so perhaps no innocents die directly because of him.)
One last thing; it seemed like the story was more focused on Krypton anyways. Superman himself was certainly the sideplot in the movie.