Like most fans, I'd love to see Clark finally take to the skies; however, there's one valid reason (from a story point) why he hasn't yet...he's still desperate to be one of us.
As much evidence as he recieves (powers, relatives, messages from his homeworld) to prove he isn't human, the Boy of Steel still desires mortality. To him, flying is the proverbial "last straw". As the Martian Manhunter says during Bizarro, "once you make this choice, there's no going back". In the end, Kal-El will have to put the farmboy aside, and embrace his heritage completely. Until then, he'll be grounded.