For months, in the corner of the screen, on all the screen transitions, on the advertising boards, on the armbands, from all the commentators and pundits, advertised everywhere is 'BLM', as well as being expressly stated every time it happens, that kneeling is in support of the BLM organisation, a deeply controversial organisation. I think it's equally fair to assume that's why they booed as it is to assume that they simply hate black people until they're actually asked.
(for the bold bit) the fans aren't the ones taking the knee, it's the players. They don't have the opportunity to not take the knee, and they also don't have the opportunity to explain why since no one's asked them, it's just assumed.
(second bolded bit) Falling into the trap of just going by the name here. If the tori's started calling themselves the 'anti stepping on puppies party', would you suddenly start supporting them because we all know killing puppies is wrong and that's the only thing that matters about them now? And would you start denigrating anyone who didn't support them as wanting to kill dogs because of their name? Or would you correctly say, it's only a name, sure people agree with the idea that stepping on puppies is wrong, but they still have all these awful policies and we want to vocal show our opposition to them.
People take the knee to follow Kaerpernick's example, and he specifically did the action originally to protest against systematic racism. That's what all the sportsmen and women are supporting, that's what 90% of the people who wear the BLM message on their clothes believe in.
The actual Black Lives Matter group/organisation, no of course you don't have to like or promote them. But you don't seriously think people who are taking the knee and believe in the BLM slogan genuinely know the ins and outs of the organisation? If you have a problem with the organisation, simply don't take the knee and give your reasoning whenever questioned about it after. Booing people are who are taking the knee and , in their way, spreading anti-racism ideals, that itself is nothing other than racism because you're literally airing your dislike for an anti-racism message. If you think otherwise there's really no helping you.