The film's title in Japan is Basu Otoko, or "Bus Man." I suspect the title is a play on "Train Man" (Densha Otoko 電車男), a popular Japanese TV series, whose titular character is also a nerd like Napoleon.
In the series, Train Man gets his nickname from a woman he rescues from the unwanted advances of a lecherous drunk on a crowded subway train. (Not having seen Napoleon Dynamite, I have no idea how the bus fits in, but the Japanese distrubutors of the film obviously sought to tap into the popularity of "Train Man" by coming up with a similar title.)
The rest of the story concerns Train Man's bashful attempts to woo the young lady. For advice on how to approach her, he turns to his network of fellow otaku (nerds). As word of Train Man's brave endeavor spreads, he becomes something of a hero to the otaku community, who shower Train Man with emails and text messages of hints and encouragement.
"Train Man" is also one of the first shows to introduce Japan's TV viewers to otaku slang and the various abbreviations used by young people when text-messaging each other via cellphone. (For various reasons, text messaging is now far more popular in Japan than computer-based email.)
Incidentally, "Train Man" began as a book, which was is actually based on a true story.