Not really,as long as u didn't interfere with the common people's closest customs and traditions and religion was one of them,in the middle age feudal society they didn't give a damn who ruled the country,they would have to pay tax to the zamindar as well as the iqtadar.So the muslim rulers mostly fought the political elite and their forces,But when intereference by force in the masses , this was attacked like under aurangzeb he unleashed a people's war beginning in maharashtra,then spredaing over punjab and in jat areas too.After killing sambhaji by treachery aurangzeb in 1689 must have thought he had won,indeed the maratha political leadership was finished the infant rajaram had fled to jinjee castle now under siege.But actually this is where the downfall began as now the people's war was unleashed on the mughal army which was raided to death by the various maratha commanders acting independently.Aurangzeb had to retreat from the deccan in 1707 a broken,failed man.
So force was not used because the rulers well knew by dealing with the princes and feudal lords they could indirectly control the land,but if they tried to interfere in the life of the common people and try mass conversions over the huge breath of the country,mass rebellions and guerilla struggle would be the end of it.
This is exemplified by the quote of the wazir of sultan illtutmish who told a group of muslim theologians who asked the sultan to give the hindus choice of islam or death,that it was a ludicrous idea which was unfeasible as the muslims 'were as few as salt in a plate of rice'.