The problem is, you've got the likes of the Daily Mail 'educating' readers that the BLM are a nasty organisation and for them the association is now ingrained (which is I believe what Nick was trying to explain).
Take a look at the tone of the headlines on virtually every BLM article on the Mail website -
Black Lives Matter: News and Updates on Murder Investigation | Daily Mail Online and look at the votes on their article about the supposed political aims of BLM UK -
Revealed: The avowed aims of the British arm of Black Lives Matter Yes, I know the articles are likely to be written to please the types of people who sign up to the Mail website, but those numbers are depressing. Sadly it seems some people will now have been brainwashed into believing BLM is bad and whether they're racist/ignorant/uneducated/easily led, some will boo players taking the knee.
I don't have an answer of how to solve it. Banning fans will make others more militant and defiant and more likely to boo. Stop the knee and it seems like the racists are winning.