I love and support the ACLU and disagree strongly with some of their positions.
No one is asking the EFF to agree with everything RMS says. However it's quite ironical that the EFF deviated from its stated goal of protecting free speech [1] on the Internet and joined the lynch mob trying to cancel RMS. This does cast the EFF in a negative light since now there's speech that the EFF likes and speech they don't. As long as there's such a dichotomy, it's hard to take an organization claiming to defend free speech seriously.
Also, there should be a higher bar for them because they're a faceless organization attacking RMS. If RMS attacked them, as individuals, I might agree to some equivalency.