Almost all Muslim rulers in India were secular. This they were in their own interest, for the vast majority of their subjects were Hindus. So if they persecuted Hindus there would be revolts and turbulences regularly, which no ruler wants.
Thus, the Mughals, Nawabs of Avadh and Murshidabad, Tipu Sultan, Nizam of Hyderabad etc were almost all thoroughly secular. For instance, the Nawabs of Avadh used to celebrate Holi, Dussehra and Diwali, organize Ramlilas, etc and give respect to all religions. Tipu Sultan used to give annual grants to 156 Hindu temples ( see online ''History in the Service of Imperialism by B.N. Pande'' ).
Akbar used to hold discussions with people of all religions, and give them respect (see my judgment in Hinsa Virodhak Sangh vs.Mirzapur Moti Koresh Jamaat online and 'Akbarnama').He propounded and practised the policy of Suleh-e-Kul, i.e. Universal Toleration of all religions ( at a time when Europeans were massacring each other in the name of religion ). His son Jehangir used to regularly meet the Hindu sadhu Jadrup, and hold discussions with him ( see 'Jehangirnama').
The controversy is about Aurangzeb. I discussed about him with many Professors of history in Aligarh Muslim University and Allahabad University. Strangely enough, The Professors of AMU with whom I discussed Aurangzeb, and who are Muslims, regard Aurangzeb as communal, while the Professors of Allahabad University, who are Hindus, regard him as secular. Which is the correct view ?
My own view is that more research is required.
On the one hand there is evidence to show that in Aurangzeb's time grants were given to several Hindu temples, e.g. Mahakal temple at Ujjain, the Chitrakoot temple, etc.( see online 'History in the Service of Imperialism', which is a speech given in the Rajya Sabha by Dr. B.N. Pandey, former Professor of History of Allahabad University and Governor of Orissa ). Details of the grants to Hindu temples in Aurangzeb'e reign can be seen there. Many of Aurangzeb's army commander's e.g. Raja Jai Singh were Hindus.
I had been to Bikaner a few years back. A part of the Maharaja's palace has been converted into a museum. I went to that museum and saw there a letter by Aurangzeb to the new Maharaja of Bikaner, who was a young man whose father (the previous Maharaja) had just died. Aurangzeb writes to the young Maharaja consoling him, and said that he could understand the loss of one's father. He concludes the letter saying that the young Maharaja should regard Aurangzeb as his own father, and if he needed anything he had only to inform Aurangzeb.
Now the point is that if Aurangzeb hated all Hindus would he have written such a letter ?
On the other hand, the fact cannot be denied that Aurangzeb reimposed jeziya on Hindus, a tax which his great grandfather Akbar had revoked. When I mentioned this to the Allahabad University Professors ( with whom I discussed Aurangzeb) they said that Aurangzeb needed money for his wars. Now if Aurangzeb needed money for his wars he should have imposed a tax on everyone, why only Hindus ?
The charge against Aurangzeb is that he demolished several Hindu temples e.g. the original Kashi Vishwanath temple, which is now the Gyanvapi mosque, standing next to the present temple built in the 18th Century by Maharani Ahilyabai Holkar. In fact the rear wall of the Gyanvapi mosque has Hindu carvings, which are clearly discernible.
Which is therefore the true Aurangzeb ?
My own view is that he was somewhere in between, but more research is required. While he was a very honest man earning his living by making caps, he also had some bigotry in him, which was a departure from the policy of his forefathers, and because of this bigotry he antagonized many Rajputs, Marathas, Sikhs, etc which hastened the demise of the Mughal Empire.
. After his death in 1707 within a few years the Mughal Empire's size was reduced to Delhi and its suburbs only ( ' Saltanat-e-Shah Alam, Az Dilli ta Palam').
Though Aurangzeb was a totally honest man ( he earned his living by making caps), he seemed to lack the great quality which Akbar had, of accomodating everyone and pursuing a tolerant and flexible, instead of rigid policy. Akbar realized that India is a country of great diversity, and so only a tolerant, flexible and accomodating policy can keep the Empire together. This realization, evidently, Aurangzeb lacked.
However , this is only my tentative opinion, and more objective research is required by experts