The flat call on the flop here is fine but it's a bit of a gamble. By flat calling he probably thinks you are drawing, probably with the As, therefore if a spade hits on the turn you aren't going to get paid. By raising the flop you give yourself more chance to get paid unless he's the sort of pussy that always fears suited flops too much.
I don't think there was any value in raising on the river with the paired board, wouldn't blame you for calling here though.

PF if you're going to re raise with AKs, which is a nice play, especially when you have position, don't min re raise, I'd pop that up to at least 6 or 7.