From the flashbacks we've seen, it appears that Dean basically raised Sam. So much of their family dynamic makes so much SENSE after seeing this episode, because to Sam, John would have always been this shadowy, distant figure in the background of his life -- someone who protected him but also lied to him, someone he loved but didn't really know. Whereas Dean was the one who fed him and played with him and fought with him and spent all day, every day, with him. "Troubled little punkboy mommy" ... *hee*.