This is a great question. Let me answer is by mentioning one incident that has caused great controversy. It is called l'affaire du voile (the veil affair) in France. In the 90's many Islamic students were expelled from school, because they were wearing head scarfs in public school. This caused a problem, because the French government stated that they are a secular government and did not want to bring religious practices into the secular sphere.
This action, of course, caused a huge controversy and bitterness in the Muslim community. From 1994-2003 there were over 100 female Muslim students who were expelled from school. Some Muslims girls had to go to Catholic schools to be able to wear their veils. In this instance, the church was more tolerant than the secular state.
These actions might seem small, but the Muslim community saw these are attacks on their way of life.