It's about more than just avoiding a thunk on the noggin. Showing the sole of your shoe or throwing shoes is a sign of extreme disrespect in the Arab world, according to the above-linked Chron article. There's an imbedded CBS news clip in which the shoe bomber's statements are translated and in which Bush says "so what" if he threw a shoe and he didn't feel the least bit threatened anyway.
I wonder if he knows about the extreme disrespect part? He probably doesn't have to - I doubt such things are important to his world view.