Just b/c it was only a segment of the Muslim leadership that drove the movement does not diminish it's religious basis. Their fears were based on religious grounds & it was also supported by a segment of the religious leadership. Yes, at first the movement focused on parity within a single sovereign state no a separate one but even then they wanted parity with Hindus based on religious grounds & they wanted more of a loose confederation than a centralized union.
Even if they were the minority from the coreligionists, so what? Their basis for separation was religion. You can deny it all you want & bring in landlords & whatnot but religion was the driving force behind the country's founders & the rallying cause of their movement.
Besides, how can anyone looking at the situation today say that they were wrong & Maulana Azad was right? Wise & farsighted unlike the naive & foolhardy Indian Muslim leadership is more like it. We have our problems today but at least they don't include being lynched to death b/c you're a Muslim & quite frankly your guys' problems aren't that much different either so it's not like we would be better off with you.
In any case, Jinnah is on record saying multiple times that he wants a state based on ISLAMIC law. Granted, he and some other founders were more modernist in their view but in the end, in their view ISLAM was to be the basis of the state.