The human brain tends to be structually consistent between the genders. We all have the same number of lobes and complex structures. The difference is our life experiences. Our brain is hardwired based on these experiences. If you come from a musically inclined family you may end up being an auditory learner instead of a visual learner because of the auditory nature of your upbringing. These kinds of experiences impact the developing brain. We actually develop different nerve pathways in the brain depending on our life experiences. So if you rough house with your son and have tea parties with your daughter, their nerve pathways are going to look a little bit different. The son's brain may learn to crave physical exertion while the daughter's brain learns that being quiet and calm is best.
This is a complex question. A very helpful way to look at this question is not only by examining biological differences, but also by looking at sociological perspective. In other words, the differences between men and women may not be rooted in biology or genes per se, but on account of social differences. For example, if a women is expected to act a certain way or think in a certain way due to society's pressures , then perhaps this pressure is the determining factor. To think along these lines may challenge biological assumptions or at least mitigate them a bit. Finally, without this angle, no biological argument will be strong.
Fact is that there are not many basic differences between the way men and women think. Most of the apparent differences between men and women are more because of the different role men and women typically perform in the family and in society rather than because of their mental make up. The only significant differences between thinking of men an women revolve around impact of emotions and relationships on their thoughts and actions. This kind of differences also, though significant, are not drastic.
Further, there are no known physiological differences between brains of men and women that cause this kind of differences in thinking of men and women. As a matter of fact there are no known significant differences between brains of men and women.