I have heard this kind of argument before, especially the oft-repeated scaremongering propaganda that "Muslims will outnumber Hindus in India in a generation". I had demolished this latter canard quite simply and comprehensively, using nothing more than a spreadsheet and census data of the last four decades. However, variants of this inexplicable majoritarian insecurity keep surfacing and never seem to die.
But their argument didn't completely convince me either.
I am not a believing Hindu. I consider religion to be nothing more than ideology, which is a set of ideas that possesses a person's mind, and which need not make any sense to a rationalist, or even be internally consistent. Ideology can come from a variety of sources. Looking for motive purely in scripture or in a narrow school of doctrine is naive, because the links from a person's ideology to religious scripture are not always straightforward. It's important to examine the murderous ideology and see where it is derived from.
There is a scriptural basis for intolerance in Islam, and there is simultaneously scriptural basis for tolerance. It is a genuine contradiction, and the contradiction is resolved one way or the other depending on interpretation. Thus, the term "jihad" could be interpreted either literally as violence against unbelievers, or as an internal spiritual struggle. Believers in each ideology claim to be the correct interpreters of their scripture, and consider the other group to be misled.
Extreme punishment for minor transgressions, of the kind encountered in the Quran, is also found in the Old Testament, but no modern interpretation of Christianity gives this any credence, even though there is no formal repudiation of these verses either. There are, however, other examples of intolerance, such as the injunctions against homosexuality, which continue to divide believing Christians. Hence Christianity too exhibits a striking dichotomy in ideology in spite of basic scriptural unity.
Sometimes, there have been creative reinterpretations of the faith itself, when placed under pressure from materially more powerful external viewpoints (e.g., the 19th century reinvention of Hinduism by Swami Vivekananda and Dayananda Saraswati on account of pressure from British sociologists as well as missionaries).
There are thus two distinct Hindu ideologies. One of these successfully combines the native Hindu tradition of philosophical tolerance with the modern sensibility of egalitarianism. The other, equally successfully, combines the negative elements of social orthodoxy and majoritarian insecurity. The latter is increasingly seen in Indian society and mirrors the rise of the BJP in Indian politics. It is this ideology that is responsible for instigating violence against religious minorities.