Muslims had some deep rooted insecurities post 1857, which was mainly their own fault (lack of education, ambition, drive; which the Hindus had in abundance). Which is why Hindus dominated politically, socially but Muslims didn't. Sir Syed's Aligarh movement started to bear fruit with a certain section of Muslim society, whereas the other section of society got influenced by the Deobandi movement. Anyways in the 1900s, through Sir Syed's efforts, the Muslim community for the most part had recovered from their insecurities, & were ready to 'compete' in India, working alongside Hindus. These people who worked alongside Hindus were for the most part progressive Muslims, not the ones influenced by Deobandi radicalism.
But certain events transpired in the 1920s & 30s that were not based on assumptions, & showed them that the issues of communalism inside India were too deep-rooted, & would always be there.