Going all in

[Soyuz]

As someone pointed out, if they'd made their set of Jacks or Queens they'd have bet reasonably big pre-flop so I think you could have ruled that out. Two pair is always a possibility but you have to ask yourself what the odds of that are. In my opinion you definitely should have gone all-in with pocket Aces with that flop. The fact that you were low-stacked should have made that a no-brainer for you.