[phydaux]

Pre-flop is fine. Post flop you failed to protect your hand or extract value.

Once the flop comes and you make middle set, there are three possible situations:

1) Your opponent has a made hand that you beat (likely).
2) Your opponent has a made hand that beats you (NOT likely).
3) Your opponent is on a flush or straight draw (likely).

Since the two most likely situations have you currently ahead, then you want to extract value. Since it's also possible that your opponent can catch up and overtake you, you want to protect your hand. Betting accomplishes both of these.

Don't check the flop. Bet out. All the check-raise does is inform the villain that you have a real hand and let's him off cheap if he has air. Bet at least 2/3 the pot to deny correct pot odds to draw. A pot-size bet is even better.

Same deal on the turn. Same deal on the turn - You're betting partly for value because you are likely ahead and partly to charge your opponent too great a price to draw.

On the river, it's read dependent. Since you say you don't have a read, well, you're getting better that 2:1 for a call. But it would have been much better to bet more and get all-in earlier in the hand.