He wasn't stupid, I don't think anyway; he just figured you wouldn't be in there with J 9. (Although you might have been in there with A J. But again, most players, even smart ones, don't expect you to flop a straight when you need non-connecting cards to hit it, and there were pre-flop raises that should have weeded you out.) He probably thought you had something like top pair and top kicker, or maybe a diff. two pair than his... hell maybe even the same two pair.

It's hard for any opponent to read a made straight when the cards needed to make it are kind of strange.