My head is telling me this is a 2000AD one-off, like a Future Shock, although I suppose it could have been Starlord or Tornado.
The synopsis is that there's a boy who spends his whole life dreaming about being the pilot of a space-going passenger craft. However he can't because all the pilots are tall, handsome, square-jawed and so on, and he's a complete six-stone weakling and ugly as sin, albeit very skilled.
However he triumphs in the end because it turns out that these ships are actually piloted by guys like him, hidden in the bowels of the ship and plumbed in to the computers, and the good-looking fly-boy types are actually all as dumb as rocks and just there for show, and to make the passengers feel comfortable.
Does that ring any bells at all?