The real reasons are obvious - it's a political symbol whether they'd like to rewrite the script and pretend it isn't, one which supports the people who want statues of Churchill torn down and tried to set fire to the British flag.
99.9% of the people booing have no problem with opposing racism; they simply disagree with the method because it has extra strings attached.
Wondered what your source is for the 99.9%.
I would suggest that "Black Lives Matter" just means that to nearly everyone taking the knee. They are not tearing down Churchill's statue, or burning the Union Flag. Such stereotyping really seems dangerous.
Last June 2020 figures were announced that 135 arrests were made across 200 Black Lives Matter protests in the UK, which featured roughly 137,500 people. That makes up 0.1 per cent of total protesters. In that same month, between 100 and 128 people were arrested for a counter-protest organised by Britain First. Twenty-seven police officers were reportedly injured across the BLM protests.
I am quite pleased when overpaid and cushioned professional footballers come together and demonstrate they have some sort of conscience and awareness of real ills in society. The US history of slavery is very different from ours, but we set the trend with slaves when North America and much of the Caribbean was a British Colony. The injustices (and yes, black Africans sold black African slaves to Europeans) have lasted for many generations. We all need to be part of the solution.
Taking the knee seems to me to be a symbol of a wider willingness to embark on that process.
For myself, I do think most of those booing were racists. There is of course no simple correlation. But there is is an unfortunate, and small, racist strand amidst English football supporters. They were drowned out by those who applauded.
Peace and love anyway.