From reading this forum I think there are four reasons (and before I go on I should make clear I've really become a fan of Karen this year, so none of the below apply to me!)
1. Some people are holding a grudge against her for the whole row with Ola thing. Ola is (or was, given the amount of grudge holding that's now going on against her) a popular pro, despite her husband, and a lot of people rushed to take her side when the story leaked, without any clue as to what actually happened. Generally I find it strange how readily a lot of posters on here believe the tabloid press, and as a result are entirely unwilling to give people the benefit of the doubt. It was the same when James Jordan first joined the show - some people still dislike him purely because of what happened with Georgina, ignoring how good he was with other partners in the intervening 8 years!
2. Karen and Nicky's partnership in her first series wasn't particularly popular, and didn't seem to be that strong a partnership, plus a fair few people didn't rate her choreography. I think for some she turned it around with her attitude when she got Dave last year, and for others with her choreography this year, but I think some still remember her as trying too hard in her first year (which in a way was understandable given it was her first year). Plus she was a new pro, the only new pro and replacing Katya, all of which meant a fair few FMs were never going to like her no matter what she did.
3. Some find her exuberance this year after she and Mark get 8s and 9s annoying, which is fair enough - each to their own in terms of personality preferences. I think she got a bit of unfair criticism on Halloween though, when she was basically just keeping in character! Some people prefer understated and lack of emotion, so for those people pros like Karen, Kevin and Janette are always likely to be annoying.
4. Some people don't like Mark, and some of those appear to then lump Karen in with Mark and be equally dismissive of her. Again, each to their own in terms of liking and disliking contestants, but it does infuriate me when people can't manage to separate the pro from the celeb - disliking the partnership is one thing, but it doesn't automatically translate into dislike of the pro!
There may well be other reasons, but those are the ones I pick up from reading the forum.
I can understand her personality not being to everyone's taste, no-one will ever please everyone (and there are pros I haven't taken to that the majority seem to adore, like Iveta). Personally I didn't like her with Nicky, I thought she didn't particularly shine, but she did a fantastic job with Dave last year and their partnership, despite being the 'joke' one, was hugely endearing in my opinion. And I think she's doing a sterling job with Mark this year, and it's the first time I've been really impressed with her choreography.
Yes, she's a bit over-excited at times, but I'd much rather have that than the disinterested vibe I've been getting from some other pros this year, and I find her hilarious and endearing on twitter and in interviews, so she's fast climbing my list of favourite pros (and all despite me still not really liking Kevin)