After 1857 Baghawat in India, Syed Ahmed Khan felt that Britishers think that Muslims were the majors cause of that Baghawat. So he disagrees with that analysis and thought that reasons were different and if he is able to get point across with Britishers, Government might better treat Muslims.
One of the major reason was that British Government was not "inclusive" for Indians. Other reasons is that Britishers failed to understand the culture and religion of people.
This book was meant to ease the blame of agitation on Muslims during failed India's War of independence of 1857. So The writer tried to please English by calling it a revolt and use somewhat bitter flattery to convince them that not all Muslims joined this cause and many joined it because they have no other options left. After all due to the absence of some settled Authority for past 150 years, people were switching loyalities whenever they saw it fit.