EFF is not "endorsing" Bitcoin in the sense usually meant; they're saying they'll accept donations that way.

The Activism Director of EFF wrote a substantial blog post on Bitcoin, calling it "a step toward censorship-resistant digital currency". Earlier, they had another post listing Bitcoin as a project that "digital activists" should contribute to.

ETA: Even without these explicit endorsements, it seems obvious to me that a prominent activism/lobbying/legal organization does not just do something like accept donations in Bitcoin without considering what kind of signal that sends.