Severus Snape was the Potions Master during most of Hermione's time at Hogwarts. He was also the Head of Slytherin House, and tended to openly show preferential treatment for the students of his own house, while being quick to criticise and deduct points from Gryffindor students. He was particularly unpleasant towards the trio, and regularly punished and verbally assaulted Harry and Ron for their poor to mediocre performances in his class. He could not do the same to Hermione, as she was the best student in the year and instead mocked her for things like being an "insufferable know-it-all," once even snidely insulting the size of Hermione's teeth. Despite his pre-existing dislike for Gryffindor, Snape's treatment of Hermione likely had more to do with her close friendship with Harry. Despite this, Hermione was still seen to defend Snape on occasion when Harry and Ron blamed him for evil deeds which occurred in Hogwarts, like setting the troll in the dungeon and trying to steal the Philosopher's Stone in Harry's first year. After Dumbledore's Death, she like many, believed that Snape was a coward who killed a man who trusted him more than anyone. It is unknown exactly how she reacted to learning of Snape's true motives and allegiance, but given her personality, it is highly likely that she came to both forgive her former Professor's cruelty, and even admire him for his bravery.
While non-canon, Snamione is very probably pairing in fanfiction.