You should check out the research of Gimbutas on that subject -- she's the one who's amassed rather exhaustive amounts of Neolithic evidence arguing for a cult of a mother goddess.
However, it's not quite as simple as all that. There was a cult of the goddess... a goddess... some goddess... which was widely revered in Europe (notice how this discussion somehow gets expanded to the entire world, I don't know why since the evidence is European and Near Eastern) -- anyway, that's not to say there were NO GODS.
It doesn't have to be either/or, it could be both.
Admittedly there are not god figures back at the beginning.
A second phase of this theory focuses on the pre-classical, pre-hierarchical states. Two lines of argument here:
1) There are a heck of a lot of myths where powerful early female divinities get usurped/overthrown by male gods. The female goddesses sometimes get vilified, demoted, or distorted into witchy/sinister figures. If taken seriously, it may be vestigial memory of a change in religion.
Or is it? Maybe it's simply justification for later sexual inequality. Nonetheless, a few examples:
-- Tiamat destroyed by Marduk
-- Apollo slaying the Python of Gaia and taking over her oracle at Delphi
-- Zeus, upon learning a child of him and Metis will overthrow him, resists sleeping with her (for a change) and instead EATS HER. Athena is born out of his skull, and declares herself born of man not woman, so she promotes men over women (at least in Aeschylus)
-- Many of the human women Zeus dallied with were originally local divinities, assimilated to the Olympian pantheon through a sort of forced marriage. Inscriptions and early evidence is fragmentary, but it's amazing how many of 'em turn out to be goddesses at the start.
2) Then there's the archaelogical evidence, which is more mixed. However, at least in Greece, there really IS a strong suggestion that early goddess cults got squashed. Examples:
~ Helen of Sparta was worshipped as a tree goddess and invoked in early Doric marriage hymns. Later, ironically, she becomes the marriage-breaker and a slut in classical mythology. There are still odd hints of her earlier divine status in Homer, though; her magical singing and weaving reminds us of Circe (who's on the way to demotion/distortion/vilification but not quite there yet)
~ Ariadne was also a local goddess, traces of which remain later in the Eleusinian mysteries (wife of Dionysos)
~ An amazing number of temples of Zeus rest on the foundations of older temples of Hera, back before she was shrew-i-fied
~ There is truth in the all-important Delphi myth. A sanctuary of Gaia is under the foundations, plus, down in the valley below, there's an Athena sanctuary plopped on the ruins of another part of the Gaia sanctuary, with Mycenaean period goddess figurines buried there
~ The Minoan snake goddess is all over the place in early art. Where'd she go?
~ Linear B tablets have Dione, Artemis, several other goddess whose names escape me now. But also, surprisingly considering his legend, Dionysos, telling us that we can't always take myths of where/when gods come in literally.
The latter again points to the idea that there were gods and goddesses, at least in the Greek region, early on.
So change the emphasis slightly: goddesses had greater stature earlier on. Minoan frescoes suggest women more equal to men, but otherwise our evidence for human as opposed to divine gender dynamics is too sketchy (at least in that area of the world) to say much.
Mind you, I really only know Greece and Rome well, Egypt and Mesopotamia somewhat -- oh yeah, one of the earliest pieces of literature in the world was written by the priestess Enheduanna, I think she was Sumerian? (can't remember when writing came in). There may be much or different evidence for other parts of the world.
My website (link in my sig) has a lecture touching on this subject by Dr. Chris Downing, as a matter of fact. She's written a widely-read book on The Goddess: Mythological Images of the Feminine and many other works, but unlike some of the wishful thinkers out there, she's actually a classical scholar and scholar of religion.
