disappointing 45th place finish, hand in question here.

[pokerraja]

i just finished 45th in a $33 mtt at PP. over 1000 entrants. anyways I really played solid poker for more than 3.5 hours. i was basically in average shape the whole tourney. no real stress at all till this final hand. how do you think i played it?

46 players left. average chips is 20,000. blinds are 1000/2000. Im sitting at 20,000 chips. I get dealt 99 UTG. I really wasnt sure what my best move was. I figured since i was close to only 10 big blinds left, its either a raise all in or fold preflop. now is this a good move? So i raised all in. I would of been very happy to just win the blinds. but i get called by the button, who barely has me covered. He flips over AQ os. i hit my set on the flop, but the turn and river brought running spades to give him the nut flush, and again, i taste an ugly loss. it has been nothing but bad beats for me real late in the tourneys for last couple of weeks.\

now im second guessing myself and wondering if this could of been avoided? If i just raise 3 or 4 times the BB, I dont want to give a AK or J10 a cheap flop. thats another reason i raised all in this situation. so how would you guys of played this hand? thanks.