In a secular society people are worried when someones allegiance to an outside influence such as religion, takes precedence over their loyalty to that country.
When zealotry supercedes patriotism you have the recipe for revolution, and France has a history of civil unrest e.g., the storming of the Bastille. When you look at the readiness of the French to take to the streets at the slightest excuse, it is no wonder that the authorities are wary.
This is a country that made a hero out of a man who demolished a McDonalds on the grounds that it was an insult to France's culinary traditions!
Giok