The author is making the point that American culture/society (through movies, tv, books, comics, etc.) stereotypes the NERD as someone who is smart and values education but is socially awkward and sexually unattractive. This is, perhaps, easily seen as a stereotype by adults who know it's not entirely accurate. But, he contends, the message it sends to children is more insidious. He thinks it turns them off anything 'intellectual' at a time when they need to be learning. By time they figure out that the stereotype of a NERD isn't accurate, it's too late. They're too behind in things like math and science and can't keep up. He's also tying this into the view American culture takes on the 'intellectual'.