The fact that Indian Muslims have stood up in this way is surely due, in part, to the fact that they live in, are the product of and feel empowered by a democratic and pluralistic society. They are not intimidated by extremist religious leaders and are not afraid to speak out against religious extremism in their midst.
It is why so few, if any, Indian Muslims are known to have joined Al Qaeda.
The premise that Indian Muslims feel "empowered" is rubbish. One of the two largest political parties in India -- and in Mumbai -- is dedicated to Muslim-baiting, and has never apologized for murdering large numbers of Muslims in Mumbai in the early 1990s, and elsewhere over the years.
As for the conclusion, well, I don't know what the Al-Qaeda numbers are, but here's a snippet from an old Times article:
An Indian security official who spoke on condition of anonymity because he was not authorized to be identified said the name suggested ties to a group called Indian Mujahedeen, which has been implicated in a string of bombing attacks in India killing about 200 people this year alone.