Comments are designed to notify the user they are addressed to. By default, the assumption is that they are addressed to the author of the post they are directly attached to - so the corresponding question or answer. They may also be directed at a specific user via the @ syntax, but the carry-over is that this sort of discussion is still directly related to the post it is attached to, so the post owner remains notified of those.
The reasoning that comments on answers do not propagate to the question asker is primarily noise reduction. We assume that for the most part, unless the question asker is directly in the comment exchange and the recipient of a direct address, the comments are probably directed either at the answerer or at others in the comment chain. They may not be useful to the author directly, and in the situation that they are, in most cases it should possibly result in the answer getting edited (which produces activity on the question and thus bumps it). Otherwise, they could be the equivalent of idle chatter. Since the question author's immediate attention may not be necessary, they thus aren't notified.
This becomes very relevant when you have a fair number of questions with a fair number of answers - this can result in a lot of comments in a short period of time, far more than is reasonable to have to sift through. There's no settings for "digest" notifications yet, which I figure is something people would prefer when dealing with that kind of a large amount of stuff. Otherwise, it's far less likely that comments on the answers are of immediate need for attention by the question author in comparison to the other kinds of activity.
The system was designed with the impression that comments are used to strengthen the answer by providing clarifications that result in revisions. But in practice, comments can be entities of themselves that are worth some measure of value. I could see that we could look into some kind of notification about comment activity on responses to one's questions, but it'd warrant some more analysis of the common value of such comments to decide how best to approach it without producing too much noise potential.