In that case it should pose no problem to be more active against religiously motivated terrorism, or am I wrong?
Most people tend to judge people by their actions, not by their creed. Unless a certain creed is sticking out by their actions, and it's undeniable that religiously motivated terrorism today is carried out by a lot of muslims, compared to other religious groups. See France or Vienna just yesterday.
Another issue which plays an important role in the relationships of muslims and other people is the fact that muslims demand a lot of tolerance for their group but are not really willing to grant the same amount of tolerance for the others. You can bet that this behaviour is causing a lot of tension.
Like someone has stated once: "Muslims are what the Catholics were 500 years ago".