Like Arnfinn said, you missed valuable bets here. Now, your read about villian betting ragged boards might be correct but remember - you were the preflop raiser. He is expecting you to bet. So, when you don't, your expectations of what he might do are now skewed. If you bet your set everytime on the flop, it would rarely be a mistake. If you never bet your set, it is almost always a mistake.