Probably the biggest reason is that nerds don't make any attempt to fit in. While this may seem like the same as popularity, it's not. Popularity is the goal, fitting in is a prerequisite. Many nerds don't even realize this. Some realize it but value their independence over popularity.
Another reason is that nerds are simply lacking in social skills. Social skills are learned, not innate, and they take a great deal of effort, intelligence, and awareness. The essay to some extent acknowledges this but I think it makes excuses that sound a lot like sour grapes. "Sure, we're bad at social skills -- but only because we don't care so much about them!" I think if we are all honest with ourselves, most of us would love to be good at both social skills and our intellectual/scientific/engineering pursuits.
Another big reason is physical attractiveness. If I could make the rules, being good looking wouldn't matter as much as it does. But I don't make the rules and it matters a great deal to most people. Good looks help with social skills too because good looking people get more practice. Over time that advantage builds up. This is why you don't see a lot of really good looking nerds, even though many good looking people are in fact quite intelligent.
Another reason is movies/TV. Hollywood stereotypes really affect people's perceptions of outgroups a great deal. What movies gets wrong about nerds is this: they correctly display the negatives about nerds (extreme social awkwardness) while completely glossing over the positives (brilliance). This is because most actors and screenwriters are not brilliant (other than perhaps in an artistic sense). So to the average person who learns about people from movies, nerds seem like average intelligence people who are really weird. Again, if I made the rules, people wouldn't be affected by media. Nobody thinks they are, but nobody thinks they are affected by advertising either, yet it's a half trillion dollar industry.
TL;DR: There are a lot of reasons why nerds are unpopular. And "because we don't want popularity" is not one of them.