I know everyone is annoyed about Clark not flying, I am too, but this is Smallville we're talking about here everyone. Clark has yet to master all of his powers yet, he's finally training with Jor-El, he's wearing the S, lets just be happy with that for now.
Now as to the flight thing, unless we've all forgotten Clark HAS flown before. He's floated in his sleep, he flew in Crusade. When he did fly he was KAL-EL, he saw himself as an alien not human. What the producers are saying makes perfect sense. Clark has always wanted to be like everyone else, human. In many instances, and its been said in the comics before that Lois makes him feel more human than he could ever imagine, that it would be Lois that would be the last obstacle that's keeping him from being able to take flight seems only right.
Recently in the One Year Later Superman UP UP AND AWAY story its shown that perhaps the reason it took his powers one whole year to return is that without his knowledge he was psychologically repressing them. And when they did return all he could really do was super jump until he could as he said "kick start his powers." It was also shown in Spider-Man The Other that for his entire superhero career Peter was repressing a lot more powers because he was psychologically afraid of what they'd be and what they'd turn him into.
So what Smallville is doing isn't that hard to understand, and I do understand why their doing it. It would be nice to see him fly in the last episode in the fight against Zod this season, and for him to chase him around the globe, but it may not happen.