Ah, the great Internet fallacy: "Me and my friends didn't like it, so it can't possibly be popular!"
Wouldn't the reverse of that be true? "My friends all like what I like so that means it must be popular?".
If you go by the sheer numbers of those on the Internet who write fanfiction featuring Voyager and Janeway plus factor in readers of those stories then her fanbase is larger then you guys (some of whom I'm sure aren't even Voyager fans) would like to believe.
But, as the old adage goes, why buy the cow when you can get the milk for free? Of course the fanfic crowd is going to be larger. All you need is an Internet connection to be part of that crowd. To read the novels, you actually are laying out extra money beyond that. How many people who can get fanfic stories for free will shell out their hard-earned money for the books on top of it?
What about the people who may read the books, but aren't tied into the Internet? They do exist.
Again, I think you're looking at numbers that are, in reality, a lot lower than you think they are. Going by one individual sample group isn't the best way to judge what's the real situation here.