The EFF is and has always been a political activist organization.
Of course they care about ideological concerns.
He's saying that they have ideological concerns beyond the ideological concerns you would tend to associate with the EFF (digital privacy, open source, patent trolling, etc). I for one am sad to see that this is the case. There are fewer and fewer organizations protecting civil rights without being dragged into left/right tribalism.
Those concerns have evolved away from their original mission. Not an unusual situation for organizations like this as a they shrink and lose relevance.