Sadly, this discrimination has been a part of our (Indian) society for centuries. Before Muslims settled in the Indian sub-continent, society was segregated on the lines of the caste system. After Muslims and other races/religions grew and expanded their cultures the segregation still continues. Unless there is a radical change in the mindset of the masses (groups concerned), this segregation will continue to be a threat to a truly educated and liberal society - that Syed Firdaus Ashraf dreams of.
The present level of intellect of the masses (Hindu or otherwise) prevents them from going forward as a single entity. Offcourse they (public) are the losers and the clergy along with certain sections of the political leadership profit from the public's ignorance.