This idea that many love to peddle here that Indian Hindu's hate Muslims is rubbish. The same Indianm Hindus have no issues, indeed they drool over Muslims from Iran, Arabs [UAE, Saudi, Omani, Palestinians, Afghans] so it can't be hatred for Muslims per se.
The hatred actually is for converts from lower castes of Hinduism who make the bulk of Indian Muslims. This is the same prejudice within Hinduism for untouchables, christians etc. The underlying dynamic is the Hindu caste system. It is a reminder that just because these untouchables etc or other lower order Hindu's have converted to Islam and adopted false Turkish/Arab family pedigree they can't escape from what they are. Hindu low castes.
Of course this might be the sentiment that informs this prejudice but socio-political factors have also conjoined with the underlying dynamic leading to what you see today. On top of this Hindu populists have used the India-Pak rivalry to add more fire and played on these sentiments to gain support.
Modi might talk but you don't see any Muslim hate when he is clasping the UAE royal family etc