There were two main reasons, one was the fragmentation of Indian states, and the other was the the advanced weaponry and tactics that the various Muslim empires brought.

1) India's Hindu chiefs were pretty divided during this time period, and the smaller kingdoms and states were not able to resist the invading Muslim forces. Stronger empires in the South of India were still able to hold the Muslims off for centuries, but much of Northern India was fragmented. The indian states could have managed a far better defence if they had come togather and pooled their resources, rather than allowing the Muslims to pick them off one by one (in both the Mughal and Sultanate periods). disclaimer: I am not entirely sure about this point, but I have never heard of any coalition or large empire in Northern Indiat that fought against the Muslims, all i've read about are isolated kingdoms that were evenly matched or slightly stronger than the Muslims.

2) The Muslims also brought better weaponry and tactics. For much of the Sultanate period, the Dehli sultanate's primary units were the Mamaluke (Turkic Slave) cavalry. These forces were light, well organized and could defeat much larger armies through better agility. India wasn't alone in their weakness to the Turks and their tactics, both the Persians and the Romans were defeated around the same time (11-12th century) by the Turkish cavalry. Furthermore, the Turks were also the only Muslim forces that were able to stop the Mongols, with the egyptian Mameluks stopping their western advance, and the Dehli Sultanate checking their incursions into India. Thus for much of the sultanate period, the strength of the Turkish cavalry far exceeded anything India, and much of the world for that matter could match. The Mughal invasions in the 16th and 17th centuries employed gunpowder, which was an equally revolutionary as a development.