What were the gender differences in prehistoric societies?

Most of the evidence we have has been interpreted as being indicative of a more gender neutral society at least in Neolithic times, with a few caveats: the evidence is limited, not exactly transparent, and often highly localised. The best example of this is probably the excavations at Çatalhöyük, a settlement in Anatolia, where certain indicators of a more balanced gender relationship have been noted:

lack of differentiation in male and female burials. This includes the fact that both men and women were buried in areas which denote the same status, usually under houses. Examination of the remains of individuals has found that nutrition did not appear to be substantially different between men and women, and even signs of hard or physical labour were relatively equally distributed between male and female skeletons.
art was more complicated to interpret, with various layers of the site, corresponding to various periods, placing greater emphasis on male and female figures. This suggests that roles may have been relatively fluid rather than static, and ultimately does not suggest that either men or women had greater importance or significance; most art focuses on agricultural scenes, and, as previously mentioned, the skeletal evidence suggests that men and women were both active in this field. It may be that the art is purely symbolic and does not actually portray the fact that men were more active in agricultural activities at certain times, but that they were more closely symbolically linked to it. This later changes to become more female focused with the presence of female figurines.
indicators that the family unit was not discrete and could be fluid. This includes testing of remains which has suggested that individuals, particularly children, were buried under houses along with people who lived with them but were not their biological relatives. This suggests a more communal approach to child rearing, which in turn suggests that women were not relegated to the home in order to raise their children.
the presence of multiple figurines which appear to represent female deities and a comparative lack of male deity figures. This has, on occasion, been interpreted as evidence of a prehistoric matriarchal society, but this is something of a spurious idea which isn’t really backed up by any of the other evidence; we don’t know the role that these female icons played, and we don’t know if, if the assumption that this female deity did indeed supersede any male deity is correct, this necessarily translated to the dominance of women within society as well as religion. It’s just speculation.
agriculture itself did not seem to be a determiner of gender roles at least at Çatalhöyük. Art indicated that agriculture was already in its early stages, and, as previously stated, this did not seem to affect the lack of differentiation in male and female life. Evidence suggests that both men and women spent time in the house, denoted by smoke marks on the ribcages of skeletons which researchers have linked to the smoke from fires kept burning in houses for warmth, as well as in agricultural labour. In fact, in the later layers of the site, some art depicted women growing plants and crops; again, the symbolic versus realistic nature of this art is open for debate, but it does show that agriculture was not entirely a male domain. Thus patriarchal society cannot be attributed singularly to agriculture.

Of course, Çatalhöyük should not be used as an indicator of life in any prehistoric society outside itself, as the notion of some global monoculture within prehistory is unfounded and cultural differentiation would have been vast, but Çatalhöyük is perhaps the most well preserved of such sites and it does at least offer evidence that categorising prehistory as either matriarchal or patriarchal is overly simplified.

To put together a relatively short answer to your question, although gender equality seems like a fairly good supposition, we don’t know exactly how prehistoric societies would have functioned for a few reasons. Firstly, the idea of prehistoric society is somewhat flawed, as there were hundreds of different settlements which would each have had their own nuanced identities and traditions. Secondly, the evidence that we do have is somewhat opaque and has been interpreted in various ways over the years, hence the prevalence of the matriarchal viewpoint, which continues even today amongst many feminist ‘goddess’ groups. Finally, although the evidence we do have does seem to correspond with the idea of greater gender equality, this is limited in terms of geography (as it does not encompass all prehistoric societies), period (as prehistory is a vast expanse of time and would not have been static), and quality (as evidence is often open to interpretation and discoveries are not equally fruitful at various sites).