I for one certainly do not agree that JREF is an atheist organization in the same sense & in the same way that AA is a religious organization (or, as I've stated, an actual religious cult).
They are miles apart.
If one cannot clearly see the relationship of AA to a typical religion - and also then see it's similarities to a typical cult - then one very well might not see just how different JREF is from AA (comparing the atheist dogma, for instance, with the AA dogma as expounded in the big book - oh, it appears I've lost my links to the atheist dogma! doh <sarcasm off>.
It might be helpful, in my view, for those people who see the two as similar to further study AA - go indepth at the links I provided earlier.