It can't be said for certain when, exactly, this little spat began, but one of the major ones was DC's decision to kill off Hal Jordan, wipe out the Corps and replace it with Kyle Rayner. There were backlashes before, take Wonder Woman being depowered for example (even though superheroes lose their powers all the time, taking hers away was sexist) but never before had the fans so quickly turned on the writers.
Now, Kyle was eventually fleshed out and became a well regarded Lantern in his own right. Heck, in Rebirth, which featured Hal's return as well as the rise of a new Green Lantern Corps, Hal payed Kyle the proper respect and the two even shook hands in a splash page.
You would think that having both Lanterns active and well written would squash the debate and allow all fans to be happy. You would be mistaken, I don't know how, or why, but the Hal/Kyle fanwar continues to this day. It's mind boggling.
You can't even write this off as an isolated incident as there are fan uproars across comic book fandom. Writers have decided to fight back and have often lashed out at fans. Nothing violent, but it's pretty clear that they don't think much of their fanbase.
When discussing the oft maligned One More Day arc in Spider-Man, Marvel editor Joe Quesada pretty much stated that comic readers couldn't relate to Peter because he was successful and happily married. As a way to combat this, Joe ordered that Peter lose his marriage and move back in with his aunt.
When DC re-introduced pre-Crisis characters for Infinite Crisis, Superboy-Prime was turned into a whiny brat who wasn't happy with the DC Universe as it stood and wanted to alter reality to fit his idea of a perfect DC world. So, basically, it was an unsubtle jab at the fans who often complained about how the DC Universe was turning out.
I'm not too familiar with Mark Millar's comic work, but I did see the two films based on his comic book properties, Wanted and Kick-Ass. While in both cases, a lot of things were changed (for better or worse is in the eye of the beholder, one thing that remained was a not so subtle sense of contempt for the audience.
The first movie ends with the main character breaking the fourth wall only to tell you that you suck for not accomplishing anything (how does he know what anyone's accomplished? There could be a nobel prize winner in the audience, he doesn't know).
The latter features a stereotypical comic nerd as the protagonist. He's obsessed with sex and doesn't have much in the way of a social life. Friends of mine found the love interest offensive as a fangirl stereotype, but his portrayal was much more denigrating in my opinion.
While Grant Morrison hasn't included any sort of jab at fans per se, his general attitude is to dismiss readers who don't like his work as simply "not getting it". People hail him as one of the great geniuses of comics and while some of his stuff is quite good, an equal portion is subpar and weird just for the sake of being weird.
This whole thing is just weird to me and both sides have points while also being in the wrong on some level.
First of all, everyone's talking about how comics are struggling to survive and how major changes are needed if the medium is going to continue. If things are that dire, why are you openly insulting your current consumers? That's a horrible business model if I ever saw one. Second, you're writers, grow a thick skin. You're not going to please everyone. Yes, the internet has its fair share of trolls, but that doesn't mean that you can't dismiss all criticism as such. They want us to care about the characters and spend our hard earned money to buy their books, but then get mad when we get mad at something that was done wrong. Just because someone writes a lengthy blog post detailing why a story fails doesn't make them some basement dweller who should be scorned. On the contrary, a lot of it is constructive and it could help the writers in the long term so that they can tell better stories and get more people buying their product.
As far as the fans are concerned, you guys need to lighten up. There are some epic fails in terms of story telling I'll agree with you on that, but there are a lot of times where people make a mountain out of a mole hill. It's perfectly fine to criticize and analyze a work, but try to keep it constructive. Rather than calling the writers names and telling them to die in a fire, point out why a plot element doesn't work and provide a better alternative.
As well as the fans, comic writers love the characters that they write. Editorial mandates can get in the way (and really the editors of both companies need to learn to take a "hands off" approach") but they're fans as much as we are. A fandom divided against itself cannot stand. When the writers attack the fans and the fans attack the writers, nothing gets solved and everyone ends up looking bad. Both parties end up looking petty and juvenile and it only furthers the stereotype.
Rather than widening the rift between the two, we should work on joining together to ensure the medium gets the success that it has the potential to have.