So I know this is a bit odd, since this question is a month old, but since it doesn't have any answers I figured I'd give it a shot.

Mughal treatment of non Muslims, such as Hindus, Sikhs, Jains etc... Has three phases. Under the first two emperors the Mughals acted as your standard, run of the mill Islamic conquerors. With heavy taxes and prohibitions on non Muslims, the Mughals later became far more tolerant under Akbar and his successors. Finally, the third phase in which the Mughals reverted back to harsh policies towards their non Muslim subjects; this process started under Shah Jahan and continued until the fall of the Empire.

The Mughals did face serious dissent from Hindus under their rule. Akbar the great, who ruled the Mughal state from 1556 to 1605, brought a large amount of Hindus under his control through conquest of new lands in Central India. But unlike later Mughal emperors, Akbar too a conciliatory approach to the Hindus. He, despite being illiterate, was a huge fan of theology, and any sort of academic work. He would host great debates between various religious figures at his court and would even invite Christians and Hindus to come and lecture him. Where as the earlier Mughal emperors (Babur and Humayun) had instituted the Jizya tax (a tax on non Muslims) Akbar abolished it in 1563. Akbar also granted Hindus and other non Muslim groups the ability to repair temples and build new ones if they wanted. Taxes on Hindu pilgrims were abolished. He even allowed Hindus who had been forcibly converted to Islam to reconvert back to Hinduism without any penalty (the usual penalty for this crime would have been death). Akbar even began to celebrate the very important Hindu festivals like the Diwali. So this had the effect of binding Hindus to the Empire and Hindus, specifically Rajputs became valuable servants of the Empire. Akbar actually created his own quasi-religion which in a way merged Hinduism and Islam. Called Din-e Ilahi, the religion was intended to become widespread and bind his subjects together permanently to ensure religious squabbles would not dominate his empire. Hindus became an integral part of the Empire and thus dissent from Hindu subjects was almost non existent.

While Akbar's son and successor, Jahangir would generally continue the policies of his father, Jahangir's son Shah Jahan would not. Shah Jahan was an orthodox Muslim and reversed many of the changes made by Akbar. Jahan made it illegal for Hindus to rebuild or repair temples, and he tore down all recently built Hindu temples and structures. He mandated a strict adherence to the principles of Sharia, which grated both Hindu nobles and Hindu commoners. While this is a relatively mild step, it was the first signs of the weakening of the relationship between the Mughals and their Hindu subjects. But there was no open dissent just yet.

Relations took an even bigger hit under Jahan's successor, Aurangzeb. Aurangzeb was an even more radical than his predecessor. His goal was to turn the Mughal state into a proper Muslim empire. He made Islamic law the highest law in the state, and Muslim officials and aristocracy gained massive amounts of power. Hindu nobles and the Hindu subjects were angered by this, because the Muslim officials (Ulema) were seen as very corrupt and self-serving. New edicts were issued that targeted non Muslims, massive Hindu temples that were considered sacred were pulled down. Muslim governors were told to replace Hindu administrators with Muslim ones. He instituted a "religious police" force called the Qazi, they terrorized non Muslim communities. This is where Hindu dissent starts to come in (sorry for taking so long to get here :/), Hindu traders in the important port of Surat in Western India began a mass migration after the Qazi forcibly circumcised a Hindu working as a clerk. The traders were important to the Mughal economy (Surat was the principle port in Western India in this time). They took refuge with a Hindu prefect in the city of Ahmadabad. They only returned after the Emperor promised to keep the Qazi inline and promised to protect their religious freedom. Aurangzeb was not done there, in 1679 he revived the Jizya, the tax on non Muslims. This caused riots in many cities. In Delhi thousands of Hindus flocked to the Imperial palace demanding the tax be revoked. Aurangzeb followed this up with policies aimed at his Rajput nobles. Eventually this culminated in a small rebellion by some Rajput nobles who felt the Emperor was being unfair. While the rebellion was crushed, it showed that the Emperor was now facing serious dissent from his Hindu subjects; from both nobles and commoners.

This new hard line policy against Hindus would be felt even more during the Deccan wars, when Hindu nobles were often accused of secretly aiding the Marathas and the other Hindu kingdoms fighting against the Mughals. Also there was the "Jat Revolts" of the late 1600's, while not completely Hindu in nature(since the Jats also counted a number of Sikhs and even some Muslims), the Jats did have a huge amount of Hindu recruits and they had the support of the Hindu people; who would covertly supply and shelter the Jat rebels.

After Aurangzeb the Mughal state sorta of collapsed, and while the Mughal Emperor still ruled in theory, he had very little power. So Hindu dissent would no longer have been directed against the Mughal Emperor, but the various independent states that ruled in the Mughal Emperor's name.

My main sources for this were:

"The New Cambridge History of India: The Mughals" by John F. Richards

"The Forgotten Mughals: A History of the Later Emperors of the House of Barbur" by G.S. Cheema

Technically the Maratha challenge, at least after the death of Aurangzeb came from within.

The Maratha leaders wanted better positions and powers within the mughal empire. They offered the weakened mughal emperor with military support in exchange for 'mansabdari' (please correct me if it was another position) of Gujarat, and then what we now call Madhya Pradesh and onwards. Eventually they grew powerful and took over almost all the mughal lands. They however did not depose or replace the mughal emperor. He was reduced to a puppet controlled by the Marathas, who ruled in his name.

Source : "India's Struggle for Independence : Bipin Chandra"