Ha ha, yeah, no...we're not that nice to each other. Granted, this fandom does seem to be a bit more friendly, nice, and all around good when held up to other fandoms, but oh man are there still problems.
Princess Molestia: This is a huge tumblr blog (and I admit, I find it highly amusing), and suddenly people started sending death threats and hateful messages to the creators. One blog I followed, another pony blog, posted how it was basically trash, and when fans of the blog tried to nicely counter the argument, the blogger turned on them and then started wondering why he/she was getting attacked for stating her opinion. You know, her opinion she stated by attacking someone else's work who hadn't done anything to her. It brought out a real ugly side of the blogger and I stopped following her because of it.
Twilight becoming an alicorn. Oh man, that was just funny to me. People were literally losing their minds over this. To me, I didn't care at all, but watching others post hateful messages about how the creators were ruining the show was disgusting and disheartening, because as you said, we tend to have a better image than most fandoms.
Clashes with fans. There have been so many stories about how the writers or artists for the show basically lose their temper because fans keep saying, "You can't do that! That's not how it works in this fanfiction!" One of the authors of the comics recently posted a blog about just that: fans were upset about details in the stories because said details weren't matching up with what fans had established in their own minds. The sheer arrogance and entitlement of that baffled me.
So yeah, we're not nearly as perfect as we like to think we are. I, for one, am just here for the show and the good times and I stay as far away from the drama as I possibly can.
As for why more people can't be like that--the image of accepting and nice--I don't know. People get very protective of their stuff, to the point where if you're not treating the stuff the same way they are, you're going to make them upset. MovieBob has done a few episodes on this issue.