Look at it this way. Unless you're a poor and desperate conversationalist approaching the art like a man mimicking his vastly superior chess opponent, do you really need to reciprocate such a question? I mean, would you consider it rude if the instructor did not ask likewise to the student, particularly when considering that the person in the higher position of power is obviously going to be the more interesting person to ask? Now, if we accept that the instructor did it not ask out of a compulsive "What about you?" habit, we can consider other motivations. The most obvious one to me is that the instructor was actually interested in the background of the student. So what, you may ask? Well, now I'm getting back to what I was trying to imply before. If you're dealing with a casual friend, you may know and ask of the background of the friend at one point, but ultimately your relationship with that person more than likely comes from shared interests/hobbies than anything, someone you may hang out with but for the moment rather than something grander. Unless he's a really personal friend, why does his life's story matter? I was under the impression that "Where are you from?" is basically the first step towards then asking about family, relationship status, plans for marriage, etc, the way a person may try to (not-always-so) discreetly size them up for a serious relationship. Therefore, to have someone ask as if they care will make the person being asked think they are skirting the edges of an inappropriate relationship with one in a position where such would not be permitted.
Admittedly there are a number of assumptions in the above. I'm not trying to pretend that I have by any means deductively proven that interest in where one is entirely gathered for the building of relationships. I do think that asking a question like that in that kind of scenario could at least give a strong appearance of trying to scout said relationship potential.
To add on, the student in this scenario reacted in a way that seemed slightly uncomfortable/indicative of boundary-crossing.