The Skeptic: The question seems to be whether religion is a problem or whether it is a catalyst where problems exist. Whether it is the substrate or the enzyme.
This is what I was getting at before. Even if religion is not on the X axis of a causal relationship, even if it is not perceived as the root of a problem, which I admit to be the case in (many) macro-level societal problems, what it is too often is an enabler. And it is a tool that has been used since its advent by the structures of power to mobilize and/or placate the masses (missionaries, suicide bombers, and slaveowners alike).
A large piece of what Ayaan Hirsi Ali sees as Islam's participation in women's oppression is the part it plays in a woman's individual psychology. The postponing of personal pleasure or independence simply because of the carrot of eternal life with Allah that is being dangled on the end of a string throughout their life. Her experience shows women who put up with arranged marriages and unwanted sex and beatings and whatever else they think they need to put up with in order to satisfy their religion's requirements for getting into heaven and/or dodging hell.
Now, one thing you need to understand about those who are not religious, who were not taught fairy tales during their childhood as though they are absolute truths (and those who don't believe them be damned, literally) is that for us, religion is optional. Or I should say that we understand religion as being optional, optional for everybody. It is this idea that is behind the subtitle to Christopher Hitchens' book- "Religion Poisons Everything." Religion is optional, he says, though it used to not be. We now understand so many of the things that religious ideas used to have a monopoly on explaining- disease, the diversity of life, the movement of celestial bodies, the cause of catastrophic environmental disasters.
Someone like me sits idly by while the entire global population quarrels ad nauseam about their competing fairy tales and cannot comprehend, cannot comprehend why this quarreling is necessary. It is silliness, and all the proof you need for how silly this all is is the legacy of L. Ron Hubbard.
Of course you don't agree and probably find this offensive. But its very important that you understand that wherever religion presents itself as a problem (even if it is not THE problem), wherever it is used by nasty people to mobilize otherwise good people to do nasty things, or enables people to give up their lives in search of posthumous reward, there will always be a chorus of people like Hirsi Ali and me asking why. Why do people need to cling to these books, 95% of the time with little or no knowledge of what is actually in them, outside of a handful of cherry-picked passages?
As long as organized religion is optional in living a good and intellectually, socially, and even spiritually (if you need to use that word) life, then wherever it presents a problem is a place where the problem is optional too, or a place where the problem would be less severe without the catalyst of divine authority.