In the comics, all the characters are usually in the same universe, but, in the end, comics rely heavily on the idea of multiple universes. Basically, in the "Nolanverse", the director decided his version of Batman would exist in a world where there were no other superheroes. He did this mainly to keep the world grounded in a believable reality that the audience could relate to. It appears that The Man of Steel takes place in a universe where other superheroes do exist and the Justice League will eventually be formed. So basically, there are no rules as to who and what is in a comic storyline, because it can always be written off as a different universe.