My close Indian Muslim friends openly tell me that they "like" Pakistan as their religion is followed there. Also when we see a India Pakistan match, their natural reaction to events is different. For example, in the 20-20 final when Misbah got caught in the last over, all Indians JUMPED from their seats in the TV room of our hostel, whereas Indian Muslims were just sitting calmly and clapping "for show"?
And this is the state of educated Indian Muslims, I dont know the majority of poverty stricken Indian Muslims may consider themselves Pakistanis.