That's not an "S" -- it's the Kryptonian symbol for "hope."

Sure, it looks just like the letter "S", which makes perfect sense considering 'Superman' starts with that very English consonant. 

However, Superman recently set us straight: this symbol is the House of El's family crest, a Kryptonian character representing the concept of hope. Hope? Superman? I don't see the connection (JOKING!).