I honestly can't think of many anime examples where a character was intended to be well-liked/supported, but ended up being disliked by the fans.
I have seen the opposite though - Anno intended Rei Ayanami to be creepy and disturbing, but she became a highly popular otaku icon.
Edit: Oh, wait, there was the infamous Kannagi incident.
That was a bit different than this, though, as I think this has been Mikono slowly but surely turning off fans, whereas with the Kannagi incident it was one particular revelation setting off
a bomb.
With Kannagi, the hate probably wouldn't have happened without said revelation. With Mikono, it's more of a "death by a thousand cuts" sort of deal.