Hate may be a very strong word. But we see, historians, social scientists, learned journalists and analysts getting uncomfortable with the term "Hindu". Here is a pseudo scientific, pseudo spiritual explanation for it.
Before we proceed with the intellectuals, we need to understand a few fundamentals.
1. Mind: What I mean by mind is that the little program that keeps running in our heads from a very young age. This mind continuously learns, by organizing every piece of information it gets. When any piece of information is encountered, the mind tries to match it with what is already there. If the new piece matches an existing information or extends it without a conflict, the mind accepts it and add it to the existing information. Let's say a child is used to seeing cats and if he happens to see a tiger, his mind extends the cat to include the information about the tiger. If the new item is conflicting with existing information, it may add it to an exception bucket. When more similar exceptions are collected, they are moved to the main storage. A child which is used to seeing terrestrial animals may find the first bird it sees as an exception. Exposure to more birds will make the information about birds as normal as terrestrial animals. If the exceptional information is not reinforced with more such exceptions, the exception loses its importance and isn't considered for subsequent processing.
Over a period, the mind gains its strength with more learning and second hand information, a side effect of which is creation of opinions. A cow as it gives milk, is good. A cat that steals milk is bad. These opinions give rise to ideologies - including religions.
The mind works around any information that doesn't fit in the mind's way of working. Zen Buddhists contemplate on paradoxical questions to silence the mind. If the mind can't find answers by the way it learns, accepts and rejects information, it goes silent.
2. Hindu: The term is fairly new - just a few hundred years old. The term was originally used by those from the west to refer to the people of this region. If religion is defined as a collection of diktats, issued by a prophet, Hinduism isn't a religion. The people, who are referred as "Hindus", had diktats, that were very local and had no prophet as an authorized signatory. So, Hinduism is not a religion. Is it a culture or a set of values? Does anyone have a well defined answer? I don't. Every custom, every definition of God and even the absence of God, every mode of worship, every mode of relating to a God is so flexible. In effect, it is not an ideology that can be understood, but is a magnificent organism that continuously evolves itself. Any attempt to define it would be just as accurate a blind man describing an elephant.
An expert on various ideologies can compare two ideologies, can judge impartially with one as good and the other as bad, as long as the ideologies are well defined. Semitic religions fit in these category of ideologies. Hinduism doesn't fit in such definition.
For an intellectual, even if he manages to identify a part of this magnificent organism, he knows his knowledge is only partial. He knows that there exists a lot more aspects of this organism, that it would be impossible for him to understand it in his lifetime. It is impossible to classify it as good or bad, for every good that he can see, there would be something bad about it and vice versa.
For an intellectual, his mind is his strength. He identifies himself with his mastery of information. The term "Hindu", challenges the mind and knows that the mind can't comprehend Hindu completely. This organism by its very existence undermines the intellectual's strength and identity. No wonder the intellectual would be uncomfortable with such a monster.