Of course in design it's Shaped like an S Because he's Superman but there are various comic-explanations as to why he wears it and how it was conceived
Movie: It was a Family Crest
Byrne MOS era: Plain Flat out lame Afterthought that S stands for Superman (ironically the same reason in real-life why he wears it)
Birthright: Kryptonian Symbol of Hope
Secret Origin: Krypton of Hope AND Family Crest
Pre-Crisis: A Symbol from a Dream of Jonathan Kent given to him by DC's judeo-christian god (known as "The Presence"
http://en.wikipedia.org/wiki/Presence_(DC_Comics) )
The Best has to be a Tie between The Pre-crisis and Waid's Birthright.Simple story that works in both comic book logic and real one is..
Superman is not an arrogant buffoon, he's not gonna wear an S on his chest just because he's named "Superman", there has to be a reason to it
Mark Waid's version has that reason to be that it is a Kryptonian symbol of hope, and that simply merits something to be proud of and worn) True it makes it a Kryptonian Symbol that Coincidentally looks like an S but we can use the glasses disguise logic for that, though it's not the only symbol of Hope in the DCU, there's the Blue Lantern insignia of course.
The Pre-crisis version had Jor-El seeing the symbol in a dream that he would use it on Kal-El as Superboy as though he was destined to be "The Chosen One" (Read the Pre-crisis Annual The Day the Cheering Stopped) and he would use the sword of Superman forged from the book of Genesis itself, which carries that crest as well..
It's obvious.. who would put the dream in Jonathan Kent's head but the DCU god AKA The Presence.

Geoff Johns tried to emulate Waid's Reason of a symbol of hope, however he also used the Movie's Family crest reasoning and although it does not really contradict each other.. it makes the House of El look selfish and Sanctimonious (what gives their family the right to have the planetary symbol of hope for themselves when there are also others who might have a claim to it as much as they would have)
The Worst is Byrne's version, because it's just an S because he was named Superman clark said in the final pages of MOS #1 "Pa and I came up with this unique design of a stylized S " WTF, and clark is smiling.. I'd imagine myself wearing a T-Shirt haveing a Stylized "R" for Rugal 3:16 but that maybe because of my personality
Superman is way too humble (and not that simplistic) to come up with something that he secretly hopes "Hey Miss if yopu see this symbol, be sure to be reminded it's me, just me, nothing else"