Having read the mangas and watched the movie/j-drama, I've never thought of it as Shoujo. It's definitely told from a male perspective; and while the subject is romance, it's about the male process of it rather than the female. Not even the male perspective, the otaku perspective XD
I've often thought that otaku culture transcends gender stereotypes in people (though, less so in Japan). Most of my male friends (including myself) sew and read shoujo (not necessarily as their primary genre though), and my female friends all play fighting games and read shonen jump from time to time. That a book written about the otaku experience should also blur the lines between gender-based genres seems quite natural. I would think you could totally swap the genders of Densha/Hermes and the story would still make perfect sense, including all their mannerisms.
I'm working my way through the actual novel in japanese right now actually. It's pretty fantastic! You can preview some of the novel here:
http://www.geocities.co.jp/Milkyway-Aquarius/7075/trainman.html
I should note, reading it will probably warp your japanese beyond recognition to any aside some an akiba-type XDDD