You have to ask yourself if you would feel the same if your race/religion/whatever was suddenly being targetted by excessive security. Would you accept it and say it was for the best, or would you argue that just because a minority is causing trouble you shouldn't tar everyone with the same brush?
I think the question is pointless: if it were my race/group that was carrying out religious terrorism then I would be far from surprised to find myself subject to closer scrutiny than I might like. The answer is for those ethnic/religious groupings to clean up their own acts, something which would earn them both the respect and gratitude which I think they both would like.
Pretending that such groups are not visibly obvious is to fly in the face of reality: would you suggest the security forces look the other way, turn blind eyes or simply hope the problem goes away?
Of course not all are guilty of either terrorism or violence; that was never suggested or implied. But you do have to look for trouble where you will find the ones causing it.