Simple, because those muslims follow what their clerics teach them, rather than going to the source. The clerics have turned themselves into an authority on Islam, a concept that doesn't and shouldn't exist.
You have such examples in your country too...lynching muslims because of the suspicion they have beef in the fridge ring any bells?
We have isolated examples so far, but if we continue down that path, we shall end up like Pakistan, where Shias, Ahmadis and Christians are bombed at prayer, schools are attacked, polio vaccination centres are bombed, schoolgirls are shot at and religious scholars decree that 9 year old girls can 'marry'. Pakistan's fate should serve as a warning to anyone bringing religion into politics - especially in India.
Pakistan started well ahead of India in 1947 - most of Pakistan is the well-irrigated, highly fertile Punjab and it got billions and billions of dollars in aid from its Western sponsors. Yet, India is now ahead in per capita income and other measures. It has largely been the detrimental affect of mixing religion in politics and public life.
The founding fathers of India had shown great wisdom by keeping religion out of matters of state - we need to continue on that path.