I think it would be awesome if you can generalize the idea for online lectures also (coursera, khan academy, udacity, etc). Since videos are not real time, letting students hit "confused" for certain segment of an online video will let the developers splice in a better explanation for bad parts of a video or even let them a/b test two different versions of a segment of the same video.
And also, instead of a confused button, maybe allow them to optionally elaborate on the source of their confusion? A potential solution for online videos is via timed comments (similar to how soundcloud does it, except maybe with interval of confusions instead http://37signals.com/svn/posts/1143-soundcloud-expands-the-a...)