That's a tough question to handle, but I'll give it a shot.
I believe there are several reasons, all of which play into eachother.
I've always believed in a certain sort of Wing Commander fan exceptionalism -- we're intelligent, we're well spoken, we have strong beliefs about our universe, we do excellent fan projects and so forth. We've built a very professional community, all of us. Taking cheap shots at any one product is really, really easy... and it's a lot of fun. I could make fun of elements of any Wing Commander game very easily - I'm a big sarcastic jerk.
Doing so to ourselves, though, reflects very poorly to the observer. I know we're just playing idiot when we make fun of Freddie Prinze Jr. or how the Rapiers look. Average Joe Internet, however, doesn't -- and he goes off to his terrible acronym based universe and spreads our hilarious sarcasm as though it were some kind of gospel... and then we get a new wave of cadets who are sure without even looking that there's nothing valuable in the movie, in Privateer, in Wing Commander Prophecy. And so instead of spreading this mesage of how great Wing Commander is, we get a bunch of people who only know it as "LOL hate movie OMFG".
Look at the Wing Commander livejournal community -
http://www.livejournal.com/userinfo.bml?user=wingcommander . Their 'description': "THis is a community fans for all things Wing Commander. Except the movie which should be stricken from the records of Wing Commander fandom as an insult to our intelligence and faith." I mean, what the hell is that? The fact that the movie is disliked (or loved) is *not* the defining factor of the Wing Commander universe. I'm damned proud of how well done my livejournal is and I can't even join the Wing community because of how insultingly stupid it treats the topic.
I also think it's very important to work towards finding the good in elements of Wing Commander. In 1997, the community acted like Privateer 2 was an offensive blight upon the series -- now, we treat it as a fun reference to the 'end' of the timeline... and we respect its really unique, stylistic film shoot. Is the gameplay still horribly unbalanced? You betcha -- but in the greater scheme of things that doesn't matter. We made it ours. The same goes for Wing Commander Academy -- people were just as vehement about the fact that it referred to stealth fighters and it implied that Blair and Maniac went to school together and so forth in 1996... now it's one of our crown jewels. We've learned to respect the little references, the parts of the timeline it fills out and its original-game-referential style.
How will we treat the Wing Commander movie five years from now? "LOK OMG PALADIN SHUD BE SCOTTTISH!!!!"? Not if I have anything to say about it. The movie may be completely dramatically unsound, but it has all sorts of unique things it added to the Wing Commander universe. The Handbook tells us about the early days of the Kilrathi War -- do we throw that out because we can't handle the fact that the Tiger's Claw looks different? Of course not. Do we have to hate the 'Pilgrim' thing? It gives us a fake religion -- and they even fleshed it out for no reason in a really amazing sourcebook. So many Sci Fi universes would *kill* for something like that. We need to learn to appreciate the long term effect of the movie on our universe rather than let it define us as some kind of self hating community.
If you hate the movie, it's three days in March out of a forty year war. If you love it... what's wrong with you? See, there I go. It builds a lot of history that truly doesn't hurt us.