The same reason why people are persecuted everywhere. Politics, Ideology, Culture, etc. Hinduism is not India. India is not Hinduism. We had good Muslim rulers, we had good Hindu rulers. We had bad Muslim rulers, we had bad Hindu rulers. What they do has nothing to do with what they are.

LOL! Muslim rulers were forced on Indians as were the British. Indians didn't have them and Islam isn't native to India. Heck, most of South Asian Muslims choose to first define themselves as "not hindu" and then as muslims. Are you denying that a good percentage of Indian muslims even today form a parallel society? Or 85% f the muslims voted for Pakistan.