Why does Tom think being unknown is actually good?

It's so he can go undetected as a superhero someday. Of course, that's all in Tom's imagination.

As the story opens, Tom describes himself as shy, a bit sweaty and chubby, and disinclined to "get out there," as his mom would say--meaning he doesn't like to assert himself and join conversations or social groups at school. Tom also describes himself as not too great of a reader, at least when he was younger. It's sad how he spends so much time within his own mind, imagining how he could be a superhero and rescue his crush, Courtney, who is of course not just beautiful and popular but also a skilled reader.

Well, having described himself as such a shy and unpopular boy, Tom actually claims that being unknown at school is a good thing. But his idea is less than practical; it goes back to his fantasies about being a superhero.

Being unknown is good, Tom tells us, because it's "perfect for a superhero." He goes on to explain that in his imagination, he fights marauders, rescues Courtney, and drives off with her in a flashy sports car, always taking the evildoers by surprise. That is, the bad guys never see him coming and never suspect him as a threat.

If Tom had instead opened up about his superhero ideas to his friend Jeff, then his fantasy wouldn't exist anymore ("I could hold onto everything better if I never talked about it and nobody ever knew") and he wouldn't get the joy of living out his daydreams again and again. For Tom, at the beginning of the story, at least, being unknown is good. It keeps him safely ensconced within his own imagination.