How does a Muslim woman quietly riding a public bus create any harm, or risk of harm, to the broader public good? She doesn't. 

Would the author draw the same conclusion if for “Muslim woman” in the above extract we substitute “person wearing a KKK hood”.

I suspect he might not. And, presumably, it would be on the grounds that KKK garb is a potent symbol of a racist ideology. And, as such, the wearing of it in public  does create at least the risk of harm in a society that professes to abhor racism in all its forms. 

Surely, there is a parallel argument that garb that conceals a woman's face is a potent symbol of a misogynistic mentality that cannot be tolerated in a country that proclaims the equality of men and women. 

So I suggest, with respect to the author, that there is indeed an argument that women who go about their business with their face masked do create a risk of harm to the broader public good.