I think there has almost always been persecution of Hindus in India. One example is taxation of Hindu temples and government control of Hindu temples. If mosques or churches were taxed, there would be a huge stink by the western press. Muslims can get government grants to make a pilgrimage to Mecca, but Hindus wouldn't be given a grant to make a pilgrimage of 5 miles.
Historically, Hindus were just too nice, allowing people in, not really understanding who they were allowing in, and what they were up to. They gave safe haven to Jews, early Christians, Buddhists (Where did the Dalai Lama go when China took over Tibet?) Hindus and Mother India have been overly tolerant for a very long time. During the Muslim invasions, probably the largest genocide (of Hindus) in the history of this planet, 100 000 Hindu temples were destroyed, and built over. A society doesn't forget all that easily.
So now that Modi has come along saying he will give Hindus some of the rights that Muslims and Christians have had that Hindus didn't have, it's just getting a fairer balance going.
The western (and Indian) press, for a long time, has been very anti Hindu, and I think people have been duped into believing a lot of it.
There, I said it.