Double Standard
The question being raised is not about the judging, but about fan's reaction, right? Why do fans and spectators get mad when Patrick Chan wins with a bad free skate?
If this is the question, I think the answer is simple. Chan won. We do not want our world champion to back into the title as the result of idiosyncrasies of the scoring system.
Whether someone got third when they deserved second is not so much in your face.
I agree, and people seem to be making this point that he was the champion. But IMO, if Kim or Volosozhar/Trankov hadn't competed (due to injury or something) and runners-up Kostner and the Germans were bumped up to 1st with their performances it would be just as outrageous. I also wonder what the reaction would have been if Ten hadn't skated, and Chan was 15 points lower in the FS and still won if people would still be outraged (though the answer is obvious).
As for Kostner checking off the points, I agree with those (and I'm sure V/M would get those checked off too)... but in the grand scheme of things, a fall in the SP or SD shouldn't put you in second place when others skate clean.
If Kostner went out there and doubled all of her jumps, I bet you would still get people defending a high placement due to the quality of her skating. Say she had reduced her 3-3 to a clean 3T-2T, and essentially had a jump layout of 3T-2T, 3L, and 2A - likely placing her second... people wouldn't bat an eyelid, because she skated clean with a beautiful program, and not even be like "2nd with those jumps, when others did 3-3, 3F, 2A?!"
I agree that Kostner is a wonderful skater, but it's a sport and she (and Chan/Germans/V-M, etc.) should not be propped up by PCS. Like, what's the point of any other skater even competing against Kostner (or V/M) if they have to put out a perfect skate with harder elements and hope she makes big errors in order to at least be only 1 or 2 points
behind her?
It's a sport and people should be attempting difficulty and be penalized when they make major errors. A fall in an SP or SD should immediately put you out of the top 3 if others skate clean... I don't care if the ice turns gold wherever you touch it -- you committed a major error on 1 of 3 jumping passes (not to mention, in Kostner's case, an inferior jump layout to begin with). If Chan fell on his quad in the SP, and still pulled in 90 points behind a clean Denis Ten, I'm pretty sure nobody here would be like "Well, he nailed the other aspects of his program, and is a way better skater than the others, so it's deserved." Yu Na landed 3Z-3T, 3F, 2A and Kostner did 3-3 with a fall (gifted with -2's, and the tech specialist didn't recognize the UR), 3L, 2A and was just 3 points behind her, and ahead of Murakami/Osmond who did 3-3, 3F, 2A. If people want to treat this as a legitimate sport you can't be defending people who technically falter.
I get that people here will hate Chan just for the sake of hating Chan, but at least if you're going to criticize him, apply the same criticism to other skaters who also benefit from PCS advantages over the rest of the field.