Yeah, the fact that Smallville
Clark grew up in a town full of Kryptonite is a source of concern. That'd be like a human growing up in a town littered with uranium deposits. There's bound to be Kryptonite dust in the air, in the water supply... he's probably gonna develop super-leukemia some years down the road. In fact, maybe that was part of why he had so much trouble flying.
Of course, the real reason is that the creators never expected the show to run more than 5-6 years, so when it kept getting renewed they kept having to delay his maturation and keep him in a rut far longer than intended; and in those last few seasons they were too faithful to their original intention of keeping the "no flights, no tights" rule until the bitter end. Once the show reached season 8, they should've realized it was time for a serious rethink of that policy. Although I think I read that Tom Welling himself refused to wear the costume under any circumstances.