I personally raise 2-3x BB with lower pocket pairs. Is that not recommended?
And yeah, I would've bet more aggressively on the flop so that he'd have to pay to chase the straight/flushdraw. But then, would that guy have really folded A4 or K4 if you raised a bit on the flop?
If I bet as a bluff, I should be thinking "am I getting better hands to fold? Is it likely that he will fold x% of the time to a y sized bet to make it +EV?". If I bet for value, I should be thinking "am I getting worst hands to call? Am I ahead of enough of his range that this is a good value bet?".