There is no doubt that Muslims in India lag behind on developmental metrics, but I sincerely doubt this is due to any large-scale systematic discrimination against them. Sure, there is a fair bit of casual "micro-discrimination" against Muslims but that happens to a LOT of demographic groups in a huge and diverse country like India.
This might be an unpopular and politically incorrect view, but I believe that the thing that is holding back Indian Muslims and (perhaps Muslims elsewhere) is their religion. Believing that women shouldn't step out of the house alone, or that women should wear a burqa all the time or that several important formative years of a child's life should be spent studying the Quran or an insistence on studying Arabic and Urdu instead of the local language are IMHO not conducive to succeeding in a cut-throat capitalist economy. My unscientific survey of successful Muslims that I know leads me to believe that the most successful ones are not that religious.
However, the OP makes a good point that Hindu fundamentalism might be polarizing opinions in the country. Unfortunately, you can get away with being a Hindu fundamentalist in India, but being a Muslim fundamentalist mostly leads to career suicide.