Can you provide examples? I don't feel like opting out of data collection is a very good example there.

I definitely feel like the ACLU took a turn for the worse in that direction a few years ago. I'll be sad if the EFF is also headed that direction - they've struck me as one of the only ones that's still willing to stand on principle

Being in support of free speech doesn't mean being explicitly tolerant of every possible opinion or political/philosophical/ethical viewpoint. I can assure you without any doubt that EFF is not sitting there fighting for someone to advocate for genocide, for example.

Further, defending privacy and free speech also means protecting from people/institutions which would act against privacy and free speech, i.e. the "paradox of tolerance" is very relevant: https://en.wikipedia.org/wiki/Paradox_of_tolerance