"Selective respect" for the Church?

In the New York Times Magazine, discussing anti-Muslim and anti-immigrant views in Europe, my friend Noah Feldman writes, in "The New Pariahs?":

Certainly it is reasonable for free societies to encourage immigrants to adopt their own liberal values. A Dutch requirement that potential immigrants view a film depicting topless bathers and gay couples may seem a little childish, but it is not a human rights violation, and it may even help prepare immigrants for the different world they are poised to enter. Schools should teach the values of the surrounding society, including respect for different lifestyles. Nevertheless, a hallmark of liberal, secular societies is supposed to be respect for different cultures, including traditional, religious cultures — even intolerant ones. There is something discomfiting about a selective respect that extends to the Roman Catholic Church, with its rejection of homosexuality and women priests, but excludes Islam for its sexism and homophobia.

I'm not sure how much "respect" the Church gets in Europe these days, but let's put that aside.  Let's put aside also the question whether the Church's "rejection" of women priests is usefully compared to (what appear to be) the practices and views with respect to women and their role in society of traditionalist Muslims.  It seems a mistake to overlook the fact that "Islam" is, for some Europeans, a matter of concern not simply because of its "sexism and homophobia", but because of (what seems to be) these Europeans' concerns about religiously motivated violence.  To be sure, it could be the case that some Eurpeans (and Americans) are unfairly attributing to all or most Muslims the bad acts and unsound views of a few.  Still, I think there's more going on here than just a prejudiced lack of comfort with newcomers.