I suppose it's because the franchise generates so much sincere, serious discussion amongst its fan base. I've never actually met someone who believed with frightening dedication that all of it was one hundred percent non-fiction.
Star Trek isn't the only thing to get this reputation from non-fans. I've run into similar reactions from people regarding everything from pro wrestling to old sitcoms.
For me it's just fun to discuss/debate things like movies, video games and TV shows. As long as no one gets TOO invested in it I get a big kick out of it all.