I have been to Nepal 4 times and they seem to be the most tolerant people you would ever want to meet. But I do know in some parts of India there are extremists(as is the case with nearly any religion- Buddhists the exception of course until I see proof otherwise).
We rent an apartment in Catholic Goa, and have been into neighbouring Karnataka and several occasions. Although the people are generally decent and friendly, there is a small but nasty element, some of who are members of the RSS. These induviduals want no foreigners in India, a Theocracy where the Saddhus make the laws, the ancient Sanskrit language and calendar, and the banning of all modern technology. You get the picture. I have to stress they are treated with contempt by mainstream people, and I never had any mither from them, but visitors to India should take care when travelling of the tourist spots into, isolated villages.