Of course Indians are Islamophobic. Any religionist fearful for the existence of his religion becomes phobic to the pressure exerted by the foreign religion which seeks to replace it. The Umayyad, Ghaznavid, the Mongol and the Tughlaq conquest of the sub-continent have been forgotten to time but their historic accounts remain pristine and accessible, although to some extent apocryphal, for those who wish to seek out the historical development of religion in the sub-continent. Read and expand your mind:
The Magnitude of Muslim Atrocities
Although the piece linked above is essentially the work of a Hindu hard-liner and his account of what happened is most certainly tainted with bias, the piece itself is not very far from the truth.
These conquests, and the most recent partition of India where Muslims carved out a piece of the land for their own use and welfare, has resulted in a deep-seeded hatred for Islam and its practitioners. Although you will find a majority of Hindus unwilling to accept this, perhaps in turn averring that their feelings towards Islam are of indifference and nonchalance, the truth is that Hindus will never be approving of the Islamic ideology and will always harbour feelings of disdain for it. These feelings are multiplied manifold when Hindu nationalism is taken into account.
There have been many recorded instances of internal violence against the resident Muslim population in India such as Bihar (1946), Nellie (1983), Gujarat (2002), Ayodhya (1992), Assam (2012), Bhiwandi (1984) and Meerut (1987). These violent outbreaks, although arguably provocations by the Muslim community, are essentially a manifestation of the resentment and ire which Hindus hold against the injustice wreaked by the Muslims in the middle-ages and the partition which was brokered by colonial Britain.
Hindus are most certainly Islamophobic and a large majority of them will always conceal their dislike for Islam and its followers, with the exception of online-forums such as this, in order to appear pluralistic and secular.