This is in the psyche of central and northern Indians particularly; Because they grow up hearing the atrocities of Islamic rule in north India, how Hindus were crushed for centuries by Persian, Afghan Swashbucklers. The hatred is alive, no denial. But, as usual generalizations fails. In states like Kerala or in many places of south India, Both communities are largely peaceful and are more integrated.
Another factor you must count is that, in recent years Hinduism is slowly moving under the control of Nagpur cult called RSS. RSS is born out of hatred for foreign religions viz Christianity, Islam and Judaism. They see these religions as the cause for disruption of world peace. As per RSS manifesto, anyone who embraced Christianity, Islam lost their natural privilege being the sons of the soil. Mark my words. Within 25 years, What Islam is blamed today for, is replaced by Hindutva unless Indian society crushes RSS ideology and stand with secular values.