Your so-called Ummah (muslim brother-hood world wide) is a myth. The Kingdom of Saudi Arabia (the so-called keepers of Islamic faith) are hand-in-glove) with US in waging war against their neighbouring Islamic Countries. Pakistan is also rendering necessary assitance to the Yankees.
Another myth being propagated by people like you is that "5 decades ago-Muslims were almost ruling elite" (your own words below). Once having established, the Muslim rulers were only interested in amassing wealth, filling up their harems with beautiful women, building monuments, etc. They did not care for the common muslims. Had the cared for them, there was no need for "Sachar Committee" and things like that. As it happens in any part of the world, the tagets of atrocities are the poorest of poor and the indefensible. A good majority of those who were converted by the invaders were the dalits and other lower casts among the natives of our Country. So the condition of Indian muslims are also not better than the dalits and other lower castes from other religions.
The islamic fundamentalism reared its ugly head after the success of Islamic revolution ( ? ) in Iran lead by a late religious leader. Till then the muslims were trying to integrate with other sections of the society. Now the genie is out of the bottle. It will require considerable time and effort to put that back into the bottle.