One important point which the author fails to discuss is the fact that someone who has a history of job-hopping might be bad at choosing where to work. I agree with the statement that "if you are job-hopping, you are over-qualified," except that I would add that if you are job-hopping, you need to do more research on the shops where you accept jobs. The job-seeker is responsible for making sure they actually want to work for their potential employer.
Thus, I think it is legitimate to hold job-hopping against a candidate (to some degree) because it may indicate that they will not put forth due diligence before they accept a job offer, and therefore they might be accepting a job that they don't really want.