The ideology of Islam embedded in Quran and Sunnath(Way of Mohummmad) is the problem. The Personality of Mohummad (Beheading those he disagreed with, being a 50 man wedding 6 year old Aisha) are medieval and barbaric. But Islam idealises Mohummad and asks a muslim to emulate Mohummad. Quran has ayats calling for terrorising non-Muslims, killing them and treating them as inferiors.
So whether we like it or not, India Pakistan problem will persist till Islam is discredited and people feel bad standing up for Islam.