It's not precisely Muslims who are seen as terrorists, just anything with Arabic or Middle East on it qualifies as terrorist! I'm Lebanese, I'm Christian and I have been treated like a terrorist by foreign ppl 
About the religion thing, maybe you have to take into perspective the fact that France wants to be portrayed as a country with many religions, that doesn't care about religion but only about the ppl 
So whether you practice your religion whatever it is or not, it doesnt matter over there, that's what I think from what I know
I maybe be wrong but eh *shrugs*
yeah but with sarkozy as i said its different! now people are pointing the finger at muslims and arabs! a few years ago, nobody would have mentioned that hatem ben harfa was a moderate muslim or a muslim practising moderately but now in everything, they mention the religion and the practice of people! before france was a country where you were french no matter your religion or origin! now they are saying that hatem ben harfa is french of tunisian origins for exemple and its smth people didnt care about before!
i think now some people (the president and some members of the government) want france to be seen as a christian country not a multicultural country anymore! they want to count people based on their religion or skin colour and its smth very new here and stupid imo!
yeah some people dont want to make differences btw muslims and arabs! stupid people once again!