Do they? This is the same law enforcement agency who is being spun as announcing that
white nationalism is as big a threat as radical Islam (perhaps not how I'd interpret the figures but there you go).
This is not to downplay the potential rhetoric behind this report or any biases the FBI may endemically have - I don't know. I'm not even from the USA. However, I would say:
i) Unfortunately, with so many police brutality allegations mired in quicksand and obfuscation, the FBI is very likely attempting to avoid further controversy by continually writing "alleged" or "perceptions" in their report. They are trying to avoid outright stating something slanderous that could prejudice something not completely proven. Of COURSE there is a problem with police brutality, and of course what the FBI have written comes across as if they're denying it because that's what we think as readers from the word "alleged"; but that's just the nature of the beast.
ii) Activism is not the same thing as "ideologically motivated criminal activity" on paper. In the minds of an investigator with bias unconscious or otherwise, perhaps there is - but at least in the words of a report, this isn't the case.
I worry that I'm sounding like a terrible apologist in the above, and I'm not intending to be. However, I also don't think that this report is intended to be some kind of horrific racist finger-pointing exercise; it simply identifies that some instances of domestic terrorism can occur through a twisting of an extremely positive ideology.