Maybe you just folded against AQ/KQ or a simple bluff because you showed fear on the river. Yes he might have a flush, or a straight with KJ (he might have 'felt lucky' holding this on the flop and turn).. but I'd definately bet around 1/2 pot on the river to get some information. (blocking bet)

I mean, checking on the river after a "possible flush" hits after raising all the streets before, is just asking for your opp to bluff you out of a better hand.