No country in the world has ever put down insurgency through military might or profiling. The more you profile members of a community from which insurgents arise, more alienation is generated from the same community. At least half of those who suffer ignominies become alienated from the same country in which they were born into and for which they had a good deal of affection. They are patriotic citizens who when subjected to mindless humiliation at the hands of the "state" turn radical.
It is a terrible feeling to be "alienated" in one's own country. All western nations and India in particular should be sensitive to this simple human dynamic.
As to moderate Muslims in India not speaking out, how many Hindus and Muslims spoke out and condemned the atrocities whenever they were perpetrated against each other by zealots of both religions in India?
Middle and upper classes in every society are the most risk-aversive. The state has an obligation to be moderate in unleashing the powers of its surveillance which border on persecution.