The basic premise is a little incorrect. I'm going to vastly oversimplify, but Pakistan was created in order to provide a homeland for the minority Muslims community. There was a sense that because India is majority Hindu, that the Muslims there would never receive equal political representation and would be relegated to second class citizens. For this reason, there was a push to create a separate Muslim state. Jinnah's original idea was that it would be mostly secular, but just overall friendly to Muslim principles. (Think of how people don't consider the USA a theocracy, but believe that it's founded on "Judeo-Christian ideals.)

India, however, was founded as a completely secular state. Some parties, during the fight for independence, did want it to become a specifically "Hindu" country (where Hindu also includes Jains, Buddhists, and Sikhs. The "native" religions as some viewed them). However, there is no state religion.

So, this is of course controversial and others might disagree, the basic point is that India is far more hospitable to Muslims than Pakistan is to Hindus. That's not to say that there aren't Non-Muslims that live happily in Pakistan or that there isn't a ton of communal violence and prejudice against Muslims in India. South Asia is incredibly complicated and interesting demographically, which is why I decided to get my M.A. studying the region :)

You might want to check out the book India after Gandhi for a good overview on the politics of the region over the last century.

If anyone has corrections or other insight on what I've posted, feel free to jump in!