Because it started when he decided to publicly shame a 13 year old girl. Yes, what she said was racist (calling him an ape) but at that age it's highly likely that the girl has been influenced by her parents or friends. She wouldn't hold that view herself from her life experiences, because she hasn't had any. What Goodes did in saying "Racism has a face. It's a 13 year old girl" was completely irresponsible from a grown man like him IMO. People, myself included, took issue with him heaping that kind of pressure on a young girl rather than her parents or the community in general. Children that age act that way because they have got it from somewhere - and that somewhere is what needed to be addressed - not the girl herself.
So naturally people were pissed off at the way he handled the situation and booed him for it - not because they also thought he was an ape, but because he handled the situation poorly. He then attributed THAT booing again to racism, which is so far from the reality of the situation it's not even funny. I was glad to see him retire, he unneccessarily over politicised the game at the time and his view on the situation couldn't have been anymore off the mark. Yes, we should stamp out racism but that's a pretty poor way to go about doing it. For a grown man who has most likely & unfortunately taken abuse like this in the past, he decided to shine a light on his situation by singling out a child in the process.