They claim Muslims are foreigners and have no place in India. According to them, Muslims are children of Arabs, Turks, and Persians. They are a reminder of Muslim rule of the region for 1,000 years under various empires.
Even though most Indian Muslims are converts from Hinduism and foreign blood is very low in them. So some Hindus use coercion to force them back to Hinduism which they call Ghar Wapsi. Others engage in violence in the shape of mobs for Cow protection, anti Love jihad (they claim handsome Muslims convert and marry Hindu females and they get left unmarried,) and general arson, rape, and murder.
As for Pakistanis/Kashmiris, because of our different phenotype, we stand out from them and they reserve their most vile hatred for us. Most Pakistanis are mixture of Iranic nomads and IVC population (Harrapa, Mohen jo Daro, etc.) We also have high rate of Turkish blood due to Khilji, Ghaznavi, Mughal royal blood.
This is the pseudo-historical map they have concocted of ancient Hindu realm which they call Akhand Bharata.