This article is in the same vein as that execrable Lisp article that showed up today: "Alas, poor brilliant misunderstood me, cursed by my genius and unwillingness to ~play the silly games of the lesser people who surround me~"
Also, not every person can be popular, regardless of whether he or she has any of the other nerd attributes. Popularity, by definition, requires a minority of the people to be identified as "popular", plus a large number of others who recognize them as popular (which is what gives rise to popularity).
Popularity tends to be associated with certain personality attributes related to socialization. Those who don't have these outward personality attributes tend not to be popular. Not having those attributes is, again, part of the definition of nerd.
"Why is a group of people unpopular, whose defining characteristic is unpopularity and the lack of personality traits that lead to popularity?" Gee, I don't know.