First off, the Mongols you're talking of are essentially the Mughals, because no other Mongol branch effectively tried to set up government in India. And the Mughals did manage to capture the south. There have been several others, but the control has been short lived, much like any empire in India. And if not in direct control, the southern areas have paid tributes to empires.

There is a very simple reason for this, because you have to run through the length and breadth of India to reach the South, if you are trying a pan-India empire. Traditional Indian borders (up until the British expedition to Afghanistan) run from Kandahar and Central Asia in the north & west, go well into the current Indian north east, and of course, the south.

Couple the land area with huge population and ethnicities, and you realize a good amount of time would be spent controlling these regions.

tl;dr: it was not "hard" to conquer the southern tip of India, it has been conquered several times by empires in Central/ South India, and even from the north. It was hard to create (and maintain) an empire that could control all of India.