I think you should've checked it. It's likely someone flopped it if they check raised like that (J10 maybe). If they had a set, they would have led out in fear that someone would catch it on the turn or river. Since you did bet it, I'd toss after the raise since you are currently dominated although you have a solid draw.
Since it's possible your opponent had two clubs, you most likely had seven outs, and less if he had a str8 flush draw. Under the circumstances I think you did the right thing, but calling an extra 1,000, depending on what the pot was at, wouldn't have been a terrible play.