Here's my theory about why fans, media, and also skaters and coaches who see themselves as martyrs often see judges as the enemy:
Judges tend to come from wealthier backgrounds than the average fan. They don't make money from judging, but having money from other sources allows the luxury of volunteering away from home many weeks per year. So there might be some class resentment involved.
Judges, by definition, are judgmental. They pass judgment on the efforts of popular skaters and often find them wanting for picky technical reasons that fans may not find of interest and that the media tend to ignore or downplay.
Some judges, by temperament and training, may be more inclined to look for weaknesses than to reward strengths. And this shows in their faces. Even judges who focus on the positive aspects and tend to be more generous with their scores may show facial expressions that look less than friendly while concentrating on technical details in the process of judging.
So when popular skaters score less well than their fans would like, the judges come across as killjoys.
Under 6.0 judging, it was pretty much up to each individual judge to place the skaters wherever they wanted. "Wherever they wanted" could be based on careful considered judgment of the merits of each performance, or it could be based on politics. Politics makes for better drama in the media coverage -- especially during the Cold War era -- so that's what the media tend to focus on whenever there was a clear reason to suspect it, and often when there was no objective reason, aside from preexisting distrust of judges as a group because of the various reasons given above.
A tradition developed of spectators booing low marks for performances they enjoyed, or booing marks that appeared to be driven by politics rather than matching
All these reasons still exist under IJS, except that the actual judging panel has much less control of the eventual results than under 6.0. Still, many fans, and journalists, don't really understand the different contributions of the technical panels and of the effects of the rules and the scale of values. So it's easier to continue attributing all the negative effects in skaters' scores and placements, and in the kinds of skills that are and are not encouraged and rewarded, to "the judges" as a generic term meaning all those officials who have power over the results. If the sport is perceived as moving in an unwanted direction, "the judges" must be to blame, as usual.