I think it's because of how poorly it was told. You had Goldberg lose the title the night before and a lot of people didn't think the time was right. Then he is supposed to get his rematch but can't get back from the police station which is literally across the street from the arena. Then you get the fingerpoke of doom. I think it was just too much at once and rubbed people the wrong way.
Personally I had no problem with Goldberg losing. It had to happen at some point and like a lot of faces, it is more exciting to have him chance the title. With the fingerpoke, I think they could have done it better. The concept was fine - "ha ha, we fooled you again" - but maybe they should have waited a week so the fans cooled down a little. Also think Hogan's delivery was bad - had he just kept going instead of doing that pause so everyone had time to figure out what was happening, it would have worked better. Plus it was a meaningless thing to do. You could have put the nWo back together without it, Nash could have stayed champ and feuded with Goldberg instead of Hogan. I think people see it as nothing but a way to get the belt back on Hogan and it ticked them off. Can't say I disagree in that aspect - there were better ways to get to their goal than to do that.