An antihero isn't necessarily a "bad guy" in the sense of a lawbreaker, but in the sense of someone who's unfriendly, mean, disreputable, or generally a jerk. Dr. House is an antihero, for example. Alan Shore from Boston Legal was an antihero, and so was Denny Crane, depending on your sensibilities. Indeed, lots of shows today seem to center on protagonists who are unbearable jerks.
Still, I would agree that it's an overstatement to call Mulder an antihero. He wasn't a jerk or a cad, just an obsessive nerd. He was an anti-establishment figure, but in the sense of, as you say, a noble underdog rather than someone who callously ignores society's rules like House does.
Still, I would agree that it's an overstatement to call Mulder an antihero. He wasn't a jerk or a cad, just an obsessive nerd. He was an anti-establishment figure, but in the sense of, as you say, a noble underdog rather than someone who callously ignores society's rules like House does.