Dear Vaagmi,
I am sure you understand the concept of minority in a democracy.
Democracy is simply the rule of majority. The side that won the elections is the "majority" and the side that lost the elections is the "minority". When it is said that the rights of the "minority" should be protected, it simply means the government run by "majority" should not take away the rights of those who voted against them.
In India, this definition has been completely perverted to suit the interests of people belonging to minority religions.
Even the specific constitutional guarantees to ensure protection of identity/culture/religion as you mentioned in your post is being grossly misused.
For example, the constitution prevents govt from interfering in institutions that are intended to promote culture/religion of minorities. This should apply to madrassas, churches or colleges that impart biblical education etc.
These institutes will naturally cater to the needs of the minority in sustaining and promoting their culture and religious symbols and ideology.
However, this proviso is being completely misused to run institutions that impart purely secular education. The OP casually clubs Madras Christian college with Hindu Benaras University. The similarity ends with the name. The Christian-run institutions, even if aided, can and does discriminate in favor of Christians both in appointment of students and faculty. You must be aware that recently Stephens hiked their Christian faculty quota to 40%. A hindu institute imparting secular education cannot favour hindus even if it is unaided. In this way there is blatant communal discrimination. Thanks to RTE, now hindus cannot even run schools without govt interference. Ironically people who support such discrimination are deemed secular and those who oppose are called communal.
Coming back to your post, my opinion is that the only protection that the Brahmins could rightfully seek is for running Veda Patashalas and similar institutions that help in promoting our culture and religion.
