KWED
Scratching head, scratching knee
You seem to be making the same basic error that many apologists make, conflating reasonable criticism of an ideology with dislike for individuals.My impression has been that the phrase was initially intended as a defense by Muslims and their rhetoric allies against the usual Islamophobic rhetoric focusing on the issue of jihad and Islam's reputation in the West as a religion for fanatics and terrorists.
Since then it has naturally been appropriated by Islam's worst critics; these days, the only time I see it come up is when people try to back-handedly insert Islamophobia into an argument without coming out and honestly expressing their disgust and hatred towards Muslims.
I suppose it makes it much easier to cope with being unable to reasonably answer the criticism.