Disclaimer: I have not read many Superman Comics.
In the Superman Movies and in the TV Show Smallville, Superman's iconic S was used as The El family crest.
Was this original intention?
I originally thought that the name "Superman" garnered the S.
Then if you listen to the old Superman radio show, it was a boy who gave him the name "Superman" based off of the S he was wearing.
So this ends up as big "chicken in the egg" question:
Which came first, the "S" or the Superman?
From the Wikipedia on Superman logo:
Initially, the S-shield had one meaning: S for Superman. One of the first alternative meanings was presented in Superman: The Movie, in which it was not an S, but rather the S-shaped Coat of arms of the House of El. After the Superman reboot story The Man of Steel, the symbol's story was that it was designed by Jonathan Kent and was derived from an ancient Native American symbol. The symbol was featured on a medicine blanket given to an ancestor of the Kent family by a Native American tribe after he helped to cure them of a plague and was supposed to represent a snake, an animal held to possess healing powers by the tribe (implying that, by wearing this symbol, Superman was a metaphorical healer). In 2004, Mark Waid's Superman: Birthright series says the S-Shield is the Kryptonian symbol for "hope" *and* Superman believes it may have begun as a coat of arms for the House of El. Later, writer Geoff Johns confirmed it was indeed a coat of arms, as well as a symbol for hope.
