I sort of talk about my view on the author-audience-text relationships here, written in response to readers musing on why they liked the writing and how they didn't feel manipulated by it. http://parahumans.wordpress.com/2013/10/26/speck-30-6/#comment-49080 - it's a bit of a ramble, I was working on 3 hours of sleep, but yeah.
More specifically, I have had bad reactions, though fortunately I've not had any in areas that I couldn't fix somewhere down the road.
Early on, I changed the plot to tailor it to the audience when Von, a WFG regular I haven't seen/heard from in the last two years, said (rightly) I was putting too much focus on the school part of the story. It was limited to a few scenes, but I did end up ending the school thing earlier than originally planned, cutting a fair bit of material, with the protagonist effectively dropping out early in the story, where I'd imagined postponing that for a stretch.
I've had bigger scenarios. Two chapters that got enough of a bad response that I took them down. One I rewrote in an all-nighter, the other I removed from the story entirely. The readers were right. They weren't good. It was something fixable (ie. gutting that part of the story).
I've also had one story arc (6 chapters) which were poorly conceived. I implemented a timeskip, a leap ahead in the story's chronology, and it immediately followed an event I'd put a lot of thought into, and it was followed by events I'd put a lot of thought into, but it was poorly thought out on its own. To top it off, I had a lot of real life distractions, with my brother, his wife and his two year old staying with me for a stretch, and a two week 'vacation' with all of us in one cabin. It translated to one of my poorest arcs, and my readers still like beating that dead horse, four or five months later. But that's fixable.
At the end of the day, though, I'm writing the kind of story I'd want to read. I know myself as a reader, and I know what I like, and I know there's readers out there like me. So long as I stay true to that, I'm okay.