I would think the true answer goes back to what jamwan55 says, it was on the costume as created in the original comic strip by Misters Siegel and Shuster.
And I would think back then, stood for Superman.
Only with hindsight, and the retelling of the story from different points of view, would other writers come up with different solutions, like the symbol seen as a family emblam ( as TEAK36 points out ) in the 1970's Superman film.
The outfit itself has different origins. In one it is created by martha Kent. In Smallville, there is a mural of a duck figure in blue and red superhero outfit on the wall of the High School, and we could see that as being the inspiration.