Hindus are made agitated by the RSS ideologists (extremists) and Hindus are told, that all their failures be it caste system or lack of unity are all because of some 300 years ago Mughals ruled them, or 7 decades back British ruled them. So, like monkeys tied on knots made to dance, the RSS rulers made them go through primitiveness and creates polarization. Otherwise, Muslims and Christians had not much problem until Nov 2014 when the Guj 2002 heroes were throned to power. India's Muslims are not Pakistani apologists in general. They are more patriotic than British shoelickers and continuous mafinaama writer like V D Savarkar, whose teachings are destroying India's religious tolerance and peaceful existence.
http://stopfundinghate.org/resources/rssprimer.htm
Pakistan is a non-issue for most Muslims in India. Pakistan is a threat that is used by radical Hindus to question Muslim's patriotism towards his country. Another issue is, a Hindu see every Muslim as follower of Allah and Islamic prophet Muhammad. In RSS classes they teaches an offstage history of Islam and in that view, all Muslims are stereotyped as temperament similar to Bedouines and they (Hindutva) holds NO respect or tolerance to Islam. This has became very clear after the rightwing came into power. Same goes to Christianity, Buddhism - first being taught as a prostelyzing religion converting Hindus
en masse and second one was blamed for eating out Hinduism centuries back preventing the dream of achieving Hindu Ummah which RSS dearly sees - the geographic region from Gandhar to Combodia under Akhand Bharat. Like extremist Muslims, these radicals also are no different, perhaps more aggressive. The rightwing Hindu view of Islam can be condensed in the contents of "Voice of India" - a book which got banned in the 80's.
https://en.wikipedia.org/wiki/The_Calcutta_Quran_Petition