When reading Philosopher's Stone, it seems that Ron was extremely nasty to Hermione all through the first part of the book - worse than to Malfoy, even.
Why such a bad reaction?
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There are two reasons:
One is a general resentment felt by normal students towards know-it-alls with a smart alec attitudes. Hermione's personality is not exactly all fluffy and endearing, she does not realize how her display of raw intellect and exact attitude comes across to other kids.
'You're saying it wrong,' Harry heard Hermione snap. 'It's Wing-gar-dium Levi-o-sa, make the 'gar' nice and long.'
'You do it, then, if you're so clever,' Ron snarled.
Hermione rolled up the sleeves of her gown, flicked her wand and said, 'Wingardium Leviosa!'
Their feather rose off the desk and hovered about four feet above their heads.
'Oh, well done!' cried Professor Flitwick, clapping. 'Everyone see here, Miss Granger's done it!'
Ron was in a very bad temper by the end of the class.
'It's no wonder no one can stand her,' he said to Harry as they pushed their way into the crowded corridor. 'She's a nightmare, honestly.'
(Philosopher's Stone, Chapter 10, "Hallowe'en")
Another reason possibly hinted at by JKR in later books was the general resentment towards A-type achievers that Ron feels extra specially because of always being compared by Mrs. Weasley to Bill and especially Percy (both of whom, as we learn in the beginning of CS, recieved 12 O.W.L.s each). It's quite possible Hermione came across very Percy-like to him.
Harry had only seen Percy at meal-times so far; he stayed shut in his room the rest of the time.
'Wish I knew what he was up to,' said Fred, frowning. 'He's not himself. His exam results came the day before you did; twelve O.W.Ls and he hardly gloated at all.'
'Ordinary Wizarding Levels,' George explained, seeing Harry's puzzled look. 'Bill got twelve, too. If we're not careful, well have another Head Boy in the family. I don't think I could stand the shame.'
(Chamber of Secrets, Chapter 4, "At Flourish and Blotts")
I think it was just eleven year old infatuation and not knowing what to do about it. Peer group pressure amongst boys is still very much - girls = yuk, so if you don't feel that way, you either get ridiculed by your friends, or do something stupid to try and separate yourself from the situation. Experience has to be learned, that's what the word means.
When I was nine I had a crush on an eleven year old girl in my class (accademic year older than me - advanced class of one year was joined with standard kids from the year above). I knew I fancied her, but had no idea what to do about it - closest I could get was to make fun of her and chant silly rymes at her (with my mates) - I have no idea why I did that, but I did. It's easy to look back over 30 years and think, what an idiot now.
I think it just shows JK's understanding of the pre-teenage mind!
Well, they didn't exactly get off on the right foot did they?
Here is their very first interaction (from Harry Potter and the Sorcerer's Stone - Chapter Six, The Journey From Platform Nine and Three-Quarters):
[I will try to keep the plagiarism to a minimum; but large chunks of the text follow]
“Has anyone seen a toad? Neville’s lost one,” she said. She had a bossy sort of voice, lots of bushy brown hair, and rather large front teeth.
“We’ve already told him we haven’t seen it,” said Ron, but the girl wasn’t listening, she was looking at the wand in his hand.
“Oh, are you doing magic? Let’s see it, then.”
She sat down. Ron looked taken aback.
“Er — all right.” He cleared his throat.
“Sunshine, daisies, butter mellow, Turn this stupid, fat rat yellow.”
He waved his wand, but nothing happened. Scabbers stayed gray and fast asleep.
“Are you sure that’s a real spell?” said the girl. “Well, it’s not very good, is it? I’ve tried a few simple spells just for practice and it’s all worked for me. Nobody in my family’s magic at all..."
So she basically just walks in, doesn't say hello and puts Ron on the spot to do magic. She then boasts about how she can do magic well.
Hermione goes on to say that she's memorised a bunch of textbooks and that she hopes to be in Gryffindor, to which Ron says:
...“Whatever House I’m in, I hope she’s not in it,” said Ron. He threw his wand back into his trunk. ...
Already, Ron is not getting a good impression of Her.
And their second interaction isn't much improved.
This occurs after Ron and Harry have an altercation with Malfoy, Crabbe and Goyle on the Hogwarts Express:
... Perhaps they thought there were more rats lurking among the sweets, or perhaps they’d heard footsteps, because a second later, Hermione Granger had come in.
“What has been going on?” she said, looking at the sweets all over the floor and Ron picking up Scabbers by his tail.
He turned to Hermione. “Can we help you with something?”
“You’d better hurry up and put your robes on, I’ve just been up to the front to ask the conductor, and he says we’re nearly there. You haven’t been fighting, have you? You’ll be in trouble before we even get there!”
She's not a prefect, they don't know her from a bar of soap and yet she's already bossing them around.
“And you’ve got dirt on your nose, by the way, did you know?”
She comes off a bit snooty and as mentioned in the other answers very much a know-it-all! Which doesn't strike Ron as an attractive quality.
I do not believe that it has anything to do with Ron liking or fancying Hermione; and therefore inadvertently mistreating her as boys do to girls they secretly like; since they didn't start liking each other until later in the series: When was the first unabiguous proof that Ron realized he was attracted to Hermione?
In terms of developing their relationship; it always excited me to see their gradual appreciation and then admiration of each-other; rather than just starting-off already being attracted to each-other.
You sort of don't see it coming. Most people assume that Harry would end up with Hermione, but I personally much prefer the fact that Ron and Hermione did.
Although Hermione being a know-it-all, as pointed out by DVK, irritated Ron more than his other schoolmates because of his seemingly more successful brothers, ultimately it's because Ron fell in love with Hermione.
Young boys are too shy and incompetent to deal with this. It naturally leads them to aggression due to the frustration felt over that they cannot compete with something, that something being a "phantom enemy" of an unacknowledged feeling he neither admit nor understand.
The very evidence of his feelings is his irrational aggression towards the girl.
These are the reasons:
It's a means of disguising his real feelings of being attracted to her but not feeling worthy. In other parts it's representative of his frustrations when other boys showed an interest in her.