The answer is obvious : because music triggers memories. So when a theme is unforgettable, it is bound to be associated to a character or a story. Reusing it allows to create a sense of continuity and coherence. When you change a well established theme, it generally means that the main character or the mood of the franchise will be changed.

Indeed John Williams created some great themes (Indiana Jones, Jurassic Park, Star Wars, Harry Potter, Jaws) who fit characters or situations so well, it seems impossible to imagine the franchises he began without them.
It's not an exclusive John Williams thing. The James Bond Theme is used since dr No by all composers who worked for the franchise (except Michel Legrand in Never Say Never Again for copyright reasons), and the Godfather themes were used in the third picture after Nino Rota death, amongst others...

There is also cases were the use of themes in popular franchises were less consistent. The theme created by Goldsmith for Alien was re-used in the second movie but not for Alien 3 and 4. Of course, the "Alien" theme was never as popular as "Superman" or "Jaws" (even if it's a really great soundtrack).

Batman is another thing : the Danny Elfman theme would seemed out of place in the Joel Shumacher flicks - the Goldenthal theme was nevertheless as close as you could get without being a rip off -, and Batman Begins tried a reboot the franchise so one of the old themes would have been inappropriate to serve this purpose.

In Superman returns, working with the the John Williams themes was the right call. The movie is not a reboot. It pays his debts to the Donner/Reeve movies, and since it is a work about adoption and renewal, not using the superman theme would have been the wrong artistic choice.