What NATO commanders did discover about their Moslem troops was not very encouraging. Most of these young Moslems joined the military just for the money. They wanted to get a job, and it is very hard for immigrants, or the children of immigrants, to get jobs in Europe. The military was always looking for volunteers, but most young guys saw being in uniform as no fun at all. So many Moslems were accepted, if not welcomed. Few of the NCOs, and hardly any officers in European armies are from emigrant families. This is in sharp contrast to the United States, where there are many Moslem NCOs and officers in the military, and the commander of all U.S. troops in the Middle East and Afghanistan is an Arab Christian.
In Europe, Moslems were held in low esteem even before 911. Since then, fear of terrorists has translated into even more disdain for Moslems. This carries over into the military, where officers and NCOs often distrust their Moslem troops, or simply show disdain for them. Senior commanders recognize that they have a problem with Moslem troops, and it's not the fault of the Moslems. But changing attitudes among officers and NCOs will not be easy, nor will it happen quickly.
Many NATO countries have sent peacekeepers to Afghanistan, but have not been able to use their Moslem soldiers as well as they thought they could. It's not that NATO thought they would have a lot of linguists, as very few of their Moslem troops came from Afghanistan. In fact, most of the Moslem troops in NATO armies, were born in Europe (it was usually their parents who emigrated, most commonly from Turkey or North Africa). But it was believed that, as Moslems, they would have a better rapport with the Afghans. That did not happen. Part of the problem is that Afghans, in general, are not crazy about foreigners, no matter what their religion. They are particularly hostile to Turks and Arabs. The former, because there is a Turkish minority in Afghanistan that has long been seen as a threat to the Indo-European tribes (the Pushtuns and Tajiks) who have traditionally dominated the area. Arabs are disliked because they comprised most of the al Qaeda personnel in Afghanistan. Those al Qaeda "troops" eventually became enforcers for the Taliban, using force to encourage compliance with unpopular Taliban directives.