Your observation is akin to the following. On a whole blank page if we put a black dot in the centre and ask one to describe what they see, 99.9% people will begin describing the black dot and completely ignore the beautiful white space that exists alongside.
A few stray ugly incidents in a 1.4 billion population cannot be ruled out, yet the progress that has been achieved alongside and in spite of such incidents is the greatest reward the 1.4 billion population, including Muslims, is reaping, owing to Modi Govt's policies. There does not exist *any* State policy that incites inter-religious enmity or bias against any minority. On the contrary, there are countless policies that are specifically designed to help, foster and enhance the status of minorities.
Note, India is secular *because* India is majority Hindu. Else, you are wise enough and observant enough I presume, to gauge from recent events, what can be expected if local demographics alter significantly...hint France, Belgium, UK, Sweden, Denmark and even some places within India. Plus our neighbours Pakistan and Bangladesh where the Hindu population is all but wiped off!!