Why did muslims not want to be part of an independent india

Because they are afraid that Muslims will be persecuted by the Hindus.

Explanation:

Hindus and Muslims never quite understood each other. For Hinduism or Islamists, it is not just religion, they are different ways of life, different visions of the world.

The Hindu religion, which arose in India, revered several different gods unlike the Islamic religion, brought by conquerors, who believed in a single god and had in Muhammad his greatest figure. Not to mention that Hindus lived in an extremely hierarchized caste society, where there was no equality between individuals, contrasting with what was preached by the Mohammedan religion that all men are equal before God.

At the time of India's independence, religious leader Mahatma Gandhi (Hindu) led thousands in a peaceful demonstration against British domination, preaching his dream of a unique and independent country where all ethnicities and religions could live equally.  But the success of the party created by him (Indian National Congress) aroused in Muslims the fear that Hindus, led by Gandhi, would constitute a state ruled by their religion where they were persecuted. In this context, the Muslim League emerged to fight for the division of the region into two states, one of them being Muslims.

they wanted the u.s. to fight on the side of the central powers.