Here, in this question, when you talk about India, it doesn’t mean whole India, but various patches of the subcontinent. So, technically, entire India was never under Muslim rule for 1000 years, not even for 100 years.
Indian subcontinent was densely populated even during the time when first Muslim invasion occurred in Sindh in 711–12 CE. The Sindhi Hindu ruler Dahir Sen was defeated by Muhammad-bin-Qasim’s army.
But the Umayyad Caliphate was well resisted by Indian rulers, so they couldn’t march further into India, especially the Indus-Gangetic belt (strecthing from Punjab to Bengal). However, another invader Mahmud of Ghazni came in the 10th century and attacked Gujarat’s Somnath temple. It was looted and many locals were killed.
Again, in late, 12th century Muhammad of Ghor tried to march towards Delhi. This time the invader Ghori succeeded when he defeated Prithviraj Chauhan. The region from Punjab till Delhi was sacked by Ghurid empire. Then, the Delhi Sultanate was established in 1206, which started expanding towards UP, Bihar and Bengal.
The Delhi Sultanate at its peak was like this (which didn’t last too long):
But the Delhi Sultans couldn’t reach out to each and every non-Muslim, whether Hindu, Buddhist, Jain or tribal. There was a strong resistance to forced conversions. Timur’s invasions also caused bloodshed in Delhi, but he butchered Hindus and Muslims alike.
Then, came the Mughal Empire in 1526. Though Babur wasn’t tolerant, his reign wasn’t widespread and very short. Sher Shah Suri and Humayun were relatively not too aggressive in conversions. Akbar was more tolerant, Jahangir persecuted the Sikh Guru Anjan Dev. Shah Jahan was busy in his monument.
The most infamous bigot was Aurangzeb. He allowed regressive and orthodox laws under his regime and many temples were illegally demolished and conversions started fastening up in northern regions. But still, in southern India, there was resistance from Marathas. Even many Rajputs started revolting against him. Sikhs also took up arms.
In the 18th century, Tipu Sultan persecuted many Catholics and Hindus in Mysore. Nadir Shah and Ahmad Shah Abdali also caused troubles in northwestern parts of India. Muslim rule officially ended in India in 1857. Princely states are not to be counted.
Conclusion: Through his summary of events during Muslim rule in India, we can conclude that:
- Whole India wasn’t ruled by Muslims for 1000 years. Moreover, most Muslim rulers had Hindu ministers and soldiers.
- Forceful conversions happened in areas which had strong Islamic control. Punjab, Sindh, Pashtun regions and Bengal Subah came directly under the Muslim rulers, and hence these regions have largest Muslim populations today. Central, eastern and southern (excluding Kerala) never witnessed direct Muslim rule for a long period.
- The Gangetic belt in India couldn’t become Muslim majority due to large Hindu population. Even today, when Muslims are 45 million in Uttar Pradesh, Hindus are 180 million.
- Majority of the 210 million Muslims in India, 220 million Muslims in Pakistan and 150 million Muslims in Bangladesh have non-Muslim but Indian ancestries.