Ultimate Bet No-Limit Hold'em, $.25 BB (8 handed)

UTG ($139.75)
UTG+1 ($24)
Hero ($29.15)
MP2 ($17.35)
CO ($4.05)
Button ($8.80)
SB ($12.55)
BB ($11.35)

Preflop: Hero is MP1 with 9c, 9h.
UTG+1 calls $0.25, Hero calls $0.25, MP2 calls $0.25, CO folds, Button calls $0.25, SB folds, BB checks.

Flop: ($1.35) 9d, Ks, 3h (6 players)
BB bets $1.6, UTG calls $1.60, UTG+1 folds, Hero calls $1.60, MP2 folds, Button folds.

Turn: ($6.15) Qd (3 players)
BB bets $0.25, UTG calls $0.25, Hero raises to $3, BB calls $2.75, UTG raises to $18.4, Hero raises to $21.15, BB folds, UTG calls $0.

River: ($48.70) Jd (2 players)

Final Pot: $48.70

Results below:
UTG has Qc Qh (three of a kind, queens).
Hero has 9c 9h (three of a kind, nines).
Outcome: UTG wins $48.70.

I made a set on the flop, but just smooth-called to encourage betting on the turn, since it looked like a raggedy flop to me. I didn't think there was a straight scare card that could come ... but I was totally wrong. Not only was the Q a straight scare card, but it also completed my opponent's larger set.

So I believe I should have either bet the pot or just gone all-in on the flop.

Does anyone think the way I played it is correct?

Do you always go all-in or bet the pot in a situation like this?

(Any comments would be appreciated. Thank you.)