That's a good question. They never dealt with the "why" of Clark's fear of heights. It was just one of those delicious ironies of the show, like Clark and Lex being best friends. Maybe since Krypton had such high gravity, Kryptonians didn'tclimb that high? That's just me grasping at straws, which doesn't make much sense, since Clark is the only Kryptonian we've seen afraid of heights. Maybe it had something to do with falling out of the sky?
Or maybe he fell out of the barn when he was younger and thus afraid of heights. To develop a phobia you needed to have have a really bad experienced and sometime it still will not form into a phobia.