I prefer not to generalize about the religion as a whole and instead focus on particular interpretations and actions. But okay, in the interests of having an honest discussion here, I'll give it my best shot.
First of all, as Dr. Ali has noted, Islam arose out of a very patriarchal society, which is reflected in the
ahadith and in
fiqh (and, albeit to a much lesser degree, the Qur'an itself). It's not locked into any kind of misogynist essentialism, as Muslim feminists like Amina Wadud and Dr. Ali herself have explored, but those aspects and their modern manifestations nevertheless
must be strongly confronted.
Second, the history of Islam became inextricably linked with the scriptures of Islam, thanks to the reliance on orally-transmitted traditions as the basis for
fiqh, and the aversion to committing to paper of anything beyond the skeleton of the Qur'an until fairly recently. This makes any attempt at extricating the evolution of the religion and the unraveling of juridical interpretation from historical fact difficult, since the kind of academic and textual criticism that's part and parcel of Western scholarship effectively strays into Islamic theology. And, of course, when you start dipping your toes into questions of theology of an active religion, people tend to get antsy. This is a definite impediment to honest inquiry - I disagree with Tom Holland's thesis (which is just Hagarism repackaged), but
the MCBs refusal to engage with him and the abuse (and possibly threats) he received on twitter is a real problem.
On a less broad level, I've been highly critical of salafism and put a lot of the blame on the increasing sense of fundamentalism in the Muslim world on the monetary and religious influence of Saudi Arabia. And I particularly hate the Muslim Brotherhood and what they did in Egypt.
