The commentator reveals an old and tired attitude, which dates back to colonial days, when the British equated the Muslim League with the Indian National Congress (more on that later) and continued post-Independence where India and Pakistan were constantly bracketed together like siblings. It also points to another old, tired attitude, where in order to win points with the Muslim world, the Muslim League or later, Pakistan would be given some concession, entirely unreasonable from the South Asian perspective.
Bush said in Pakistan:
I explained that Pakistan and India are different countries with different needs and different histories. So as we proceed forward, our strategy will take in effect these well-known differences.
Whatever the actual merits of the nuclear deal (I do not know enough to weigh in) and whether the politically weak administration (approval ratings at 34%) can push the deal through Congress against the non-proliferation ayatollahs, this break with the past has to be counted among Bush's achievements. It shows he is not entirely within his private bubble world. Much as I dislike Bush, I have to grant him that.
The NPR commentator should note that India is not a non-Muslim country, it has as many if not more Muslims than Pakistan. India's heartbeat, however, is secular. The commentator would also do well to distinguish between a Muslim country and a country with an Islamic form of government. E.g., Turkey is Muslim country with a secular government. Iran is a Muslim country with an extremist Islamic government, and Pakistan is a Muslim country ostensibly following an Islamic path of "enlightened moderation".