There is a big difference between trips (What you had here) and a set (3 of a kind while holding a PP) If you were holding 99 here and the flop had come K29 instead, then you would have a set of 9's, and it would be worth going broke nearly every time.

With trips, and lots of action (like the actual hand) you need to have a pretty good read that your opponent is loose enough to commit a lot of chips with just a 1 pair hand. What about your opponent having the case 9 in his hand (definitely part of his range)? What would you think about your 6 kicker then (which doesn't play on the turn)? It looks like you are playing on Level 0, only looking at the cards in front of you. We need to get you to level 1 to really get a better idea of what your opponent could be holding.
I deliberately raised small at the start to make my continuation bet look weak - this was the kind of ideal circumstance I was looking for when I put the small raise out. I wanted him to think, he's just trying a poor attempt to bluff so I'll go over the top of him
You missed your C-Bet on the flop. And you WERE trying a poor attempt to bluff (at least Pre-flop). These are the type of hands you want to play fast, but not get attached to. You had multiple opportunities to not lose your stack in this hand, the easiest would've been Pre-flop.