I'm also puzzled by the negative reactions some people have to the film. Does the film fail to register because the "Trek" social phenomenon is unfamiliar to them, thus there's no frame of reference? I'd really like to know.
Comedy is possibly the hardest genre to get right, because line delivery, timing, direction and character shading all have to be pretty much perfect or the movie just won't be funny. GQ nails these elements -- right on the head and in virtually every scene -- and keeps up the pace by constantly moving its characters forward. Tony Shalhoub (Fred), Sam Rockwell (Guy Fleegman) and Enrico Colantoni (Mathesar) in particular are so dead-on perfect in their scenes that lack of box office and the Academy's traditional indifference to comedy are probably the only reasons these guys didn't get Oscar nods. (Okay, well, 1999 was also an incredibly strong year for American cinema.)
But GQ is also strangely moving -- particularly in the way it derives comedy from despair. The actor characters' lives are in ruins, not unlike the aliens they eventually save from extinction. Perhaps this is why -- even though the characters don't know it yet -- the two groups get along so well and why the actors make the decision to actually become their TV characters in the end. This may also be why the dismay in Mathesar's face when he learns the truth is so painful.
I suspect GQ also got lumped in with the likes of "Scary Movie" and "The Naked Gun" movies in the public's collective conscious: It was perceived as just another spoof and therefore not worthy of significant attention. I hope the movie develops enough of a cult following that it one day reaches that wider audience it deserves.