Not sure why the response was surprising: one group was protesting police brutality, and the other was protesting the exact pandemic rules that the CDC (etc.) was pushing. It would be a bit weird for the CDC to say "hey, we need to keep businesses shut down and people should stay inside, but it's cool if you want to go out and protest that requirement, in direct violation of the requirement itself".

And sure, there's a political/optics component. Disapproving of protests against police brutality would have been an incredibly bad look, much worse than disapproving of protests against pandemic safety measures. That shouldn't require any kind of explanation or evoke any surprise.