Yes, we are thinking and rational beings, and yes, we do make efforts to behave accordingly. But intelligence is a pretty recent development, evolutionarily speaking, and the deliberate building of social structures is even more recent. You can't overturn millions of years of biological development simply by force of will acquired in a couple of thousand years of social development. If we are "wired" to behave a certain way, we can TRY to consciously change that, but the wiring is always there when consciousness loses its focus and provides the "wired" behavior an opportunity to break forth. (For my part, I'm amazed that our social structures hold as well as they do when it comes to sex.)
We can find a concrete example by looking at the various known intellectual differences between men and women. Before any PC hackles are raised, I'm NOT talking about "superiority" or "inferiority," just DIFFERENCES in how we process information and act on it. Anyone with eyes is forced to acknowledge that these differences exist. If consciousness truly ruled behavior, it shouldn't matter what gender of meat the consciousness happened to inhabit. The presence of clear and obvious gender-linked tendencies toward certain ways of thinking and acting suggests that we ARE wired to behave in certain ways, and though we may make efforts to limit that behavior, we cannot entirely eradicate it. (I think a lot of people would argue that you can't even minimize it, only redirect it.)