Even if he did make a flush, you still have outs.

You can catch 10 cards which gives you about 4.5:1, or about 18%. If he has the nut flush, I'm assuming he's not going to lay it down if you catch so you can win all his chips in most cases. If he bets less than 18% of his stack, then you should definately make this call. And then theres the possibility that he doesn't have a flush and you are crushing him anyway.