There is speculation that in India cows became "sacred" as a result of being conquered by nomadic tribes who told the locals that they weren't allowed to touch the cattle which belonged to the conquerors. After many years the reasons behind this prohibition were forgotten, but the "don't touch the cows or you're in big trouble" commandment had become an unquestioned part of India's culture. I don't know if there is any hard evidence to support this, but it's an interesting hypothesis.
In the centuries after 2000 BCE came the second set of immigrants (the Aryans) from the Eurasian Steppe, probably from the region now known as Kazakhstan. They likely brought with them an early version of Sanskrit, mastery over horses and a range of new cultural practices such as sacrificial rituals, all of which formed the basis of early Hindu/Vedic culture. (A thousand years before, people from the Steppe had also moved into Europe, replacing and mixing with agriculturists there, spawning new cultures and spreading Indo-European languages).
The idea of the mixing of different population groups is also unappealing to Hindu nationalists as they put a premium on racial purity.
The most recent study on this subject, led by geneticist David Reich of Harvard University, was published in March 2018 and co-authored by 92 scholars from all over the world - many of them leading names in disciplines as diverse as genetics, history, archaeology and anthropology.