IMO Dollhouse was accused of misogyny from the perspective of people who see, in a piece of fiction, literally anything bad happening to a female character as proof of the writer's dislike of women.
Regardless of how the execution of the show turned out, Dollhouse is a fairly challenging concept, and way more challenging that anything that usually makes it on network television. Realize that it is a story where essentially the villains are the protagonists and the viewer is fed information and opinions through the lens of these people trying to justify their actions. (Or at least repress the moral complications.)
By the end of the series I was left with the impression that the events of season 2 were probably compressed down from both a second and third season outline. I wonder what kind of show it would have been if season 1 hadn't been meddled with so badly and the rest of the arc was unwrapped across 3 full seasons. In the end that's the funny thing about Dollhouse to me. It's probably my least favorite Whedon TV series... but it's possibly the most interesting
Whedon TV series.