Can't seem to avoid these type of hands

Doing well in a stars $10 MTT, 66 left and I was about 20th then this troublesum hand ruins my day.

PokerStars Game #587706082: Tournament #2220376, Hold'em No Limit - Level XIII (1500/3000) - 2004/08/02 - 20:08:25 (ET)
Table '2220376 38' Seat #1 is the button
Seat 1: J. Wrexx (62592 in chips)
Seat 3: microdisney (118580 in chips)
Seat 6: blackie9 (58289 in chips)
Seat 7: beautytown (38340 in chips)
Seat 8: ladyluck22 (26096 in chips)
Seat 9: Walt75904 (53763 in chips)
Seat 4: KewlKatt (49067 in chips)
Seat 5: tpope212 (44173 in chips)
J. Wrexx: posts the ante 150
microdisney: posts the ante 150
KewlKatt: posts the ante 150
tpope212: posts the ante 150
blackie9: posts the ante 150
beautytown: posts the ante 150
ladyluck22: posts the ante 150
Walt75904: posts the ante 150
microdisney: posts small blind 1500
KewlKatt: posts big blind 3000
*** HOLE CARDS ***
Dealt to KewlKatt [Ad Th]
tpope212: raises 3000 to 6000
blackie9: calls 6000
beautytown: folds
ladyluck22: folds
Walt75904: folds
J. Wrexx: folds
microdisney: folds
KewlKatt: calls 3000
*** FLOP *** [Ts 6h Ah]
KewlKatt: checks
tpope212: checks
blackie9: bets 15000
KewlKatt: raises 27917 to 42917 and is all-in
tpope212: folds
blackie9: calls 27917
*** TURN *** [Ts 6h Ah] [4c]
*** RIVER *** [Ts 6h Ah 4c] [Qs]
*** SHOW DOWN ***
KewlKatt: shows [Ad Th] (two pair, Aces and Tens)
blackie9: shows [Qh As] (two pair, Aces and Queens)
blackie9 collected 106534 from pot
*** SUMMARY ***
Total pot 106534 | Rake 0
Board [Ts 6h Ah 4c Qs]
Seat 1: J. Wrexx (button) folded before Flop (didn't bet)
Seat 3: microdisney (small blind) folded before Flop
Seat 6: blackie9 showed [Qh As] and won (106534) with two pair, Aces and Queens
Seat 7: beautytown folded before Flop (didn't bet)
Seat 8: ladyluck22 folded before Flop (didn't bet)
Seat 9: Walt75904 folded before Flop (didn't bet)
Seat 4: KewlKatt (big blind) showed [Ad Th] and lost with two pair, Aces and Tens
Seat 5: tpope212 folded on the Flop

Should have I protected my blind with ATo on a 2xBB raise?

I knew that blackie9 didn't have trips ( he raised/re-raised his PP), so I had to assume I had the best hand and put him on TPTK. Knowing he had a better kicker than me, the only move for me was to take the pot down on the flop. Question is will this type of scenario pay off for me or make me pay more in the future?

oh, and was Check Raising the right move in this situation, my initial thought was to see what the PFRaiser was going to do. I thought I could get him trying to buy the pot after a missed flop.

Should I have made my Top 2 pair known right away? a 15k+ bet was required to remove any flush/strt draws off the odds. I don't think It would have changed the outcome of the hand anyway.

I say it was just luck of the draw. Who is honestly going to fold AQo with top pair on that type of flop ever? Nobody. It was a good call, and you made a good flop push. He couldn't have put you on ATo. You couldn't have gotten him to fold. Luck of the draw my friend.

you got rivered - pure and simple.

as much as something like this hurts, nothing you could have done would have changed the outcome (with the possible exception of going all-in preflop, which, with AT, would be a bad move).