Annie, I wouldn't beat yourself up over it. MTT poker is a grueling experience and a lot of luck is involved. Sometimes you will make the right calls and people will hit their 2/3-outers against, and then you lose 2-3 coinflips in a row and you're out. Sometimes you'll get it in dominated and get lucky.
The key to MTT poker is not making one or two moves or laydowns particular to the situation, but making the right decision based on pot odds
and your equity vs. someone's likely range. In most cases if you have already raised with AK, and there are antes and lots of dead money in the pool, it's rarely going to be correct to lay it down just because you "put them on a pair."
Esp. if you are raising in late position vs. the BB, he is going to give you less credit and the tight BB will sometimes show up lighter than you'd expect (Don't you think he could have AQ there?).
I'm not saying you never lay down AK or avoid huge confrontations when you're flipping at best, but if you always make laydowns like this, people will start making moves on you.
The key to MTTs is getting to the Final Table with a good chip stack. IT's going to be frustrating when you play well for several hours only to bubble or barely place in the money. But your goal is always to make the FT and esp. get into the top 5 spots. Because those rare times when you do will make up for all the frustrating bustouts.
Even top pros can't always wait for "a better spot." Remember when Scotty Nguyen looked like he was going to make the final table with a great chip stack, he ended up tilting it all off in two hands and finished 11th. Allen Cunningham had to make a stand against Jamie Gold when he knew he was good but was only a slight favorite.
So don't worry about one or two decisions like these, you're going to have to keep making them over and over again; sometimes they'll work out and sometimes they won't. There's nothing you can do to control the way the cards fall.