In Japanese culture, it is important to lower yourself and respect others. As a result, compliments (even meaningless ones) are very important. Western culture shares similar hidden societal rules, although these are more commonly and simply known as "brown-nosing".
One must consider that the poor Japanese person is searching for some compliment that can be delivered in his or her English, which also has some bearing on reality. Even if they know that chopsticks aren't a Japanese invention, there is still some assumption that any gaijin must have had to study quite hard to learn to do anything Japanese. However, all Japanese people use a knife and fork at some point, so the counter-compliment is ineffective.
It is also correct etiquette in Japan to deny any compliment given to yourself. Considering the following dialogues:
Japanese Person: You speak Japanese very well.
Beginner: Thank you very much.
Japanese Person: You speak Japanese very well! (showing actual surprise)
No-longer-beginner: No, I still have much to learn.
Living in Japan, I have been complimented on all sorts of odd things. One very similar to this case is my ability to speak English well. I am a native speaker of English, and even those who do not know me will assume so by the fact that I'm caucasian. Yet I have been complimented countless times on it.
However, despite knowing this rule, I am still unable to bring myself to accept (or rather deny) the compliment that I am able to use chopsticks. Perhaps there is no perfect reply to this compliment. Perhaps it is a zen mantra.
2003-09-19 Update: Since writing this piece,
I've made a practice of asking Japanese people where chopsticks come from.
The answer is almost unanimously "Japan, of course!" among children, and generally just a confused look