Small correction: the Muslim massacre of 59 Hindu pilgrims in Godhra in 2002 helped Modi win.
The difference between Modi and the Congress is that Modi treats Muslims as equal citizens. Congress treats Muslims as superior. Muslims are not superior in any way. What is happening is that the rich upper class Muslims are keeping the poor Muslims poor so that they always have an army of violent thugs ready to riot. If you are a poor Muslim, your worst enemy is the rich Muslim who does not want you to grow less poor.