That is a bizzare interpretation of the plot. Only a small scene within a fairly large plot. Although from what I have seen of that scene (ahem.), he was not so much scared of piloting as much as scared of waring with others. His personality was essentially that of a pacifist, being a young student and all. But that is the way of similar stories. Must have your underdog who doesn't seem a match for the role. Pretty much like Star Wars or any movie with a hero in it. In fact nearly all films, anime etc will have similar issues. Just my two cents.
However nonsensical the cartoon is, its funny. So props to you!