Bearing in mind that they live in country that is far more Christian than Muslim (by a factor of roughly 50 to 1 in the US). It shouldn't be surprising that they would complain about the predominant religion, rather than that of a relatively small minority.
Were Muslims predominant, they would presumably direct their ire towards them...until a few of them were beheaded, anyway.
Your “anti-theists” of the 18th century had the same nice things to say about Mohammed. They hated the Church and so they said nice things about Mohammed. Their hatred is the reason why the Revolution turned into a bloodbath and ended in tyranny.