Catalhoyuk in Anatolia is the test case, because it produced the most cited figurines and has been excavated again with modern recording. The renewed work found that the great majority of figurines from the site are not female at all; that many are animals or ambiguous forms; that they were overwhelmingly recovered from middens and other rubbish contexts rather than from anything resembling a shrine; and that they appear to have been made quickly and discarded. A figure treated as a goddess in the older literature turns out to be one item within a large and varied assemblage whose disposal pattern does not look cultic.
The general objections are three. Identifying a female figure as a goddess rather than as a doll, a charm, an ancestor, a portrait or a teaching aid is an assumption that the object does not make for the archaeologist. A single continuous cult across thousands of years and a continent is not something the material can support, since the figurines differ enormously across regions and periods. And the argument tends to be circular, with the figurines proving the religion and the religion explaining the figurines.
Cynthia Eller has made the further argument that the matriarchal prehistory story, whatever its appeal, is not a sound foundation for a contemporary movement, because a myth that can be refuted is a fragile thing to build on. The atlas records the Mother Goddess as a useful comparative category and an unreliable historical claim, which is exactly what it is.