The "Muslim" government of Bosnia was, and is, about as secular in practice as the Communists had been. If it were simply an issue of religious toleration the Christians had no reason to start a fight.

The civil war was a landgrab by the business elutes of Croatia and Serbia - religion didn't come into it as a basic motive.

There is *now* an element of Muslim fundamentalism in Bosnia - under US tutelage, the Saudis have been trying to extend their influence. The Saudis have actually been responsible for demolishing more mosques than the Serbians did, since said mosques were acting as foci for varieties of Islam opposed to their own. The majority Islamic tendency in the Ottoman Balkans was the Bektashi dervish order, which has traditionally been associated with both socialism and the separation of religion and state.

As far as I know, the US/Saudi/Wahhabi element haven't extended their control very far yet.