In sum, Islamophobia, in the Bosnian war, was an expression of hatred directed against an ethnic group, or groups. One of the paradoxes of this is that for all the Islamophobic hatred directed against the Balkan Muslim peoples by Balkan Christian nationalists, and indeed by the anti-Muslim bigots in the West who supported them, the Bosnian Muslims and Kosovo Albanians are among the most secularised Muslim peoples in the world. Just as Jewish atheists will always be the Christ-killers or ritual slaugherers of Christian children in the eyes of certain anti-Semites, so Bosnian Muslim and Albanian atheists will always be jihadis in the eyes of Islamophobes.A long and interesting historical perspective from Marko Atilla Hoare.
I agree with his initial statement that it's incorrect to say, as many do, that religions are a matter of choice and therefore unlike race or sex and that therefore discrimination against religions are not like racism or sexism. The distributions of religions plainly correspond to geographical and demographic distributions. In this, they are more like nationality than race, and they are not a matter of simple choice. I argued this a couple of years ago during a talk I gave to the Oxford Secular Society.
The real difference is that unlike nationality religions have bodies of dogma. Sure, there can be national narratives and these can have important texts, but this isn't analogous to scripture. And scriptures can be liked or disliked, admired or hated, on rational, analytical grounds - unlike race or gender.
But scriptures aren't people, and this hatred or admiration doesn't transfer to individuals or groups without becoming a prejudice just like racism or sexism.