When you consider this religious tradition has existed for thousands of years, it is only natural to expect passions would evolve. It has even taken on a recent political aspect. If you look up what happened to Wendy Doniger after the publication of her book, The Hindus: An Alternative History, you will realise the antagonisms that exist within Hinduism and India.
In short, it goes back to the fact that Shiva existed before the Arians and the Vedas. The Arians came into India and set up the Brahmanical structure, with the pantheon of the Vedas, but Shiva, and his female consorts could not be so easily replaced - they seeped up through the overlay and became acceptable principles within the canon. Unfortunately, it was never an easy mix.
But they weren't the only 'old' deities to penetrate into the pantheon. Brahmanism itself was and remains resisted, especially in the South, and among the tribals and remote villages. They tried to draw in every god and goddess, but it always remained a questionable fit.
Today, due to resurgent Hindu identity, especially with Hindutva, many Hindus reject the whole idea of the Arian invasion. This rejection is not based on facts, but on the principle of Hindu integrity and supremacy.
But it doesn't stop there, as there are ideological battles within Vaishnavism and Shaivism. There are Hindus who reject the whole concept of a God, or anything beyond the physical. In fact, the divisions within Hinduism are far more complex than any religious tradition I have looked at.
