After presenting some information on the practice of female genital mutilation or as it is sometimes euphemistically called female circumcision, MWR at Don't Trust Snakes raises an excellent question about why religions are so consistently misogynistic.
I was going to leave a comment but quickly realized I had more to say on the topic than would fit for a comment.
Modern day religion reflects patriarchal society; the real question is why we as a species so consistently come up with male-dominated societies. There are of course lots of opinions on this subject.
The party line EP opinion is that male dominance is a function of mate preference. Women prefer taller, more muscular men while men who are taller and more muscular enjoy more mating success and research suggests they also produce more children. Men tend to be larger, pound for pound and inch for inch, than women. This sexual dimorphism, as scientists call it, contributes to male social dominance. For some statistics on how height translates to dollars and influence, check this out.
This assumes size is what determines social hierarchy. However, any cursory study of primatology shows that dominance is maintained through alliances - not brute strength. This may be true for within sex dominance struggles, but when it comes to a battle of the sexes, females who team up can sometimes assert some level of authority over a male or two for some time. The fact remains that even in so-called "female bonded" groups, males are still dominant. Very few primate societies are truly female dominant (lemurs come to mind) and they are really only dominant during the mating season.
Size matters in the animal kingdom. The vast majority of animal species are sexually dimorphic and male dominated. The two go hand-in-hand. Exceptions are for monogamous species, who don't really live in groups and therefore aren't hierarchically organized, and species in which males provide most of the infant care. In those species, male competition for mates (the thing that drives sex differences in size), is attenuated. Instead, females compete intensely with each other for males who will invest a huge amount of energy, time, and resources in infant care. Once a female secures an investing male, she ditches him and looks for another who will take care of her next set of offspring. Females in such species call the shots and have all of the power. They also tend to be physically larger, though for monogamous species, size and power tend to be distributed equally.
In the realm of animal biology, there are definite relationships between social dominance, sexual dimorphism, and brood care. Where females assume primary care of offspring, males tend to be larger and more dominant. Where males assume primary infant care, the roles are reversed.
Human patriarchy is a relic of sexual dimorphism produced by a quirk of biology - women invest more heavily in infant care than men do. Under this scenario, male patriarchy will fade around the same time women a) date and mate with men who are shorter and smaller than they are, and b) are freed from the responsibility of raising children.