I know many Muslims from India here in Saudi, and they tell me exactly how they are treated in India. Muslims, as a whole still see themselves as a different 'nation' from the Hindus. The areas are segeregated on the basis of Hindu/Muslim majority and both parties are apprehensive while treading in the other's territory. Muslims find it difficult to maintain their identity, and keep to themselves. The prejudice is not so blatant in the governemnt's policies but is easily observed in society and individuals. For instance, Indian Muslims do not eat meat from any international franchise such as KFC, Pizza Hut and so on becasue it's not Halal. One wonders why aren't the MNC's don't do anything about it knowing the population of Muslims in India. My Indian friends have various explainations for it.
Btw, I know 4 gentleman from Kerala, 2 from Hyderabad, 1 from Delhi, 1 from Bombay, 1 from Bihar and 3 from Bengal. Suffice to say, they all have the same issues and views on their life in India.