This happens in comics quite a bit. And after a while you get burnt out on "A good story is a good story." How many times must we see Spider-Man's origin retold? Why make each one slightly incompatible with the others? At what point are we not "updating" or "revising" an origin story and just doing a cash grab. Say, something like the recent Age of Ultron event. It took so long to complete the book that it didn't slot into the ongoing narrative. (I believe it came out some 2 years after it was intended to.) So the story that resulted was very distanced from the body of books being put out. Add to it that it was basically a time travel story/alternate timeline and it just became this weird book happening in its own little corner that barely touched anything happening in the vast majority of books. It could have been great, could have been terrible. Many people opted not to read it because "it didn't count." While it had some ramifications for the larger universe, it didn't advance anything, it didn't even seem like an exceptionally well crafted character piece. So it's largely been ignored. Now that's not to say the mentality is right, but after a while, investing $72 + to buy an event book that really doesn't add anything feels like a waste of money.
And the Star Wars EU is a slightly different beast. Until 1999, their continuity was fairly tight with each other. Characters hopped between video games, books, comics and young reader books. (Galaxy of Fear and the Jedi Prince books being two of the few exceptions to the continuity!) And it was marketed in that way to appeal to fans, both hardcore and casual. Almost every Star Wars novel has that handy-dandy chronology chart at the front now. And the prequels conflicted with some of that, sure, and some of the earliest books were incompatible. But they worked at it. Heck, some things in the prequels only exist because of the Expanded Universe. (Lucas was rather fond of it, too, and encouraged the expansion, to a degree. Apparently he bought the first collection of the Dark Empire comic miniseries for every LucasFilm in employee in 1993/4 because he loved it so much.) There was very much an idea that outside of a few exceptions, everything "counted" in the Star Wars EU. I remember there being a bit of an outcry when they tried to "decanonize" Coruscant Nights. A fourth book was written a few years later that then bridged the issues of CN with the wider universe. (Like the unfortunate case of "Indistinguishable..." If you're going to publish it only to basically say "Hey, that never happened" a year later, it begs the question of why publish it in the first place?)
Why do the latest Trek movies go out of their way to take place in another timeline, when it would be just as easy to not acknowledge it? They didn't want to write off the other material as "not counting." It's silly, but I think we all have these biases about what we want to read and what it should mean. I really can't stand the majority of "between the episodes" Trek books. I could frame that by saying "because they don't count" or I only "read the ones that do count." But, in all honesty, I just hate the "toys back in the box" mentality. I like forward momentum, I like the freedom to change that the Post-2001 Trek novels have embraced. As well, you could say I that I have no interest in the Star Trek online novel because it "doesn't count" toward the current slate of novels. But, really, I'm not playing the game. I'm not the audience for it. It doesn't have any relevance. May be a good story, but I have to draw a line somewhere. And if that line is "It really doesn't play into what I'd like to read and doesn't count toward the continuity the other books I'm read take place in, I can save $7."
And, as Thrawn says, it's not that hard to see why someone would be annoyed that books that many of these readers grew up reading and, have been reinforced through coy marketing, that are all interrelated, are suddenly deemed incompatible. Just last year, they released a giant book that detailed every piece of fiction put out in the EU and explained how they linked or didn't link together. It's a nice tome. But it reinforces the idea of there being a cohesive universe in which these things place. Marketing or not, people bought into it.