No, i don't see why he should raise with a flush draw(exception JT, see below), especially, when you have the ace.
I guess there're some sensible scenarios:
1. He's holding some kind of middle to high pair (small pair 6< is more unlikely, but is also possible, because he was on the button)
2. He has sth like AQ, KQ, QJ ... and has now a top pair with nut/high kicker
3. He's holding JT in diamonds, thus he has so many outs that raising would make sense.
4. He interpretes your bet as a continuation bet and tries to steal the pot..
Nevertheless i would allocate the probabilities sth. like that:
10% bluffing + 50% AQ/AK + 40% trips
AQ/KQ/QJ.. gives you a chance of about 90% to win (calculated that he has about 3-4 outs left; either another of the two queens, or an average of maybe another king/gutshot straight card...) --> 90% you win in 50% = 45%win
When he holds trips you actually can only win, by making A trips, which is:
2 outs => ~8,5%; Now the assumed probability of 40% that he holds trips X 8.5% = ~3,3%
Now you add the winning probabilities together: 10% + 45% + 3,3% = ~ 60%.
Of course with AA you can't throw your hand away, especially if he offers you sth like 2:1 odds.
With 60% winning probabilite i would also raise, just to define my hand.
As you only have left about 1400 - his raise = ~ 1000 the allin raise seems reasonable, otherwise you would be crippled. Nevertheless, if he has the trips, good luck. But the percentage is with you ♦
Rofl, that was kinda too thorough 
