They have attacked people even moslem in Nigeria. Previously, they have stated to support and pledge allegiance to ISIS
Two of the most affected provinces (Yobe and Borno) are more than 90% Muslim. But most of their previous attacks had targeted the local Christians. A large part of the schoolgirls kidnapped in Chibok were Christian. Now very few Christians remain in these two provinces, as they have migrated towards the other provinces.
Yeah it is always hard to being minority in a country, especially in religious country. They always get unfair policy by the government with the authorities, and become the target of rebels.