It is hard to believe that Muslims are specifically targetted by police and others. On the contrary, I think that they are most loud to give a political color to any misdemenour.
Take Hyderabad for instance. This place has the most chaotic traffic, with virtually no one following traffic rules. However police are clearly biased in favor of Muslims. Most muslims drive very rashly, which is the reason police fears taking any action on them. And thus the whole city sees a chaos on roads.
Most governmental organizations harass people irrespective of religion. But because the harassed individuals are muslims, they always manage to get it heard and gain political mileage. If the govt officials harass Hindus, it is not news!