While much has been discussed about the British policy of divide-and-rule while governing India (and other colonies), another fact that has not received the same attention is the enormous support received by the Muslim League from India's Muslims. Why was the Congress not able to convince India's Muslim population that they would be better off in united India?
The basic idea behind the single nation theory is that Muslims and Hindus and many other religous communities as well are all intertwined alongside various languages and religous communities into one larger cultural unit. The idea behind the Two-Nation theory is that Hindus and Muslims, due to various prohibitions against cultural exchances like intermarriage, are essentially two separate nations. Most (but not all) adherents to this theory feel that India should be for Hindus exclusively and Muslims should have their own countries.
It isn't too hard to see why the Two Nation theory is more attractive to Muslims. It offers them the chance to live in a country where they run things. All the single nation theory offers them is a perpertual life as a minority in a country dominated by Hindus.