Capping the flop is an option as well here. Both should be fine.
I guess you planned to raise the turn again and as protection isn't very effective on the flop you can go for a stronger valueplay.
Let's take a look at the turn. The A is indeed one of two cards you don't want to see but does it really makes our hand that much worse?
Which hands would he 3-bet preflop? Let's assume that he is playing by our BB vs ORC Chart (It should be near the silver charts if not please let me know.). That gives him a range of: 99+, ATs+, AJo+. Capping against this range is of course correct. 
Let's go on with the flop. His 3-bet here is changing his range a lot in my opinion. As we don't have any stats here I assume that he is not LAG so 3-betting with A-high makes no sense for him. We can remove all A-high hand. We should let AKs, AKo in as assuming that he will never 3-bet any A-high might be expensive for us.
Let's calculate that with Equilator (if you haven't seen this software you can get it here: http://www.pokerstrategy.com/software/6/ ):
Board: Ac 6c 5s 2h
Dead:
Equity Gewonnen UnentschiedenVerloren Hand
Spieler 1: 46.250 % 45.000 % 2.500 % 52.500 % QsQh
Spieler 2: 53.750 % 52.500 % 2.500 % 45.000 % 99+, AKs, AKo
46% is just to much to fold it on the turn.
Now we can assume that he is indeed 3-betting with all A-high hands in his preflop range:
Board: Ac 6c 5s 2h
Dead:
Equity Gewonnen UnentschiedenVerloren Hand
Spieler 1: 31.669 % 30.849 % 1.639 % 67.511 % QsQh
Spieler 2: 68.331 % 67.511 % 1.639 % 30.849 % 99+, ATs+, AJo+
Still way to much for folding as we get 12:1 on the turn and we win around 3 out of 10.
--> Call turn.
