at the risk of agreeing with Mexineil, I er.......agree
You have to consider what he thinks you might be holding. Raising a single limper when holding AKd, AQd (or even AJd) would fit your hand - i.e. he has to know that you could have the nuts.
Also - he closed the betting before the flop against 3 hands, getting more than 3-1 to call your raise. Plenty of players would call that in a cash game with a range of hands - he might have 99, TT (with a diamond), or somesuch hand. He might have KQ (with one or two diamonds), KTd even QTd or 98d.
He might even have an overpair and have decided to try and scare you off the pot.
His bet might make sense if he had the nuts - just trying to get more money from you, but when you have the ace, I'd put him all-in. He now has to worry that you have the nuts, or at least a draw to it.
If he has KQd you have a 32% chance to outdraw him (about 3% of that being when you fill up or make running aces). If he has QTd then you have a 27% chance of outdrawing him, or T9 where you have a 23% chance.
If he has JJ you have a 34% chance of winning and if he has 88 you have a marginally higher chance. JJ is very unlikely we would have to think though.
I don't think calling is a terrible play - he still has to be worried about the nuts, but if a blank falls on 4th then you are down to around 15% to win. If the board pairs (assuming he has the flush) then you are up to 23% again. You can make a decision based on what he does, as you have position.
Overall, all-in would be my first choice, but calling is ok.