The "you're annoying" line is one of the most misunderstood aspects of Sasuke and Sakura's relationship. One negative phrase repeated three times in their relationship doesn't equal, "I don't care about you." Especially when Sasuke also labeled Naruto as annoying on more than one occasion. Calling someone annoying doesn't mean you hate them; most people have probably found their loved ones annoying at some point or another. Sasuke calling Naruto and Sakura annoying didn't mean that he hated them and wanted to distance himself from a relationship from them altogether, it just means that he found some of their behaviors annoying. Sasuke's actions in Part I towards both of his (and I quote Sasuke) "precious comrades" shows that he does care about his teammates, even if they did occasionally drive him crazy.

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The first time Sasuke called Sakura annoying was because she was being too glib about not having parents and criticizing Naruto for being misbehaved because he had no correctional parental guidance in his life.

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While Sakura's words were out of line, rude, a bit cruel, and should not have been said, the funny thing is that despite all the hate Sakura gets for her actions in this scene, some of the things she said were right. Sakura was right that Naruto got away with behaviors that the others kids' parents would punish them for. Sakura is saying she envies Naruto's situation, because in her mind Naruto gets to do whatever he wants without parental correction and without repercussions, and while Sakura criticizes his character because she believes his orphaned status made him selfish (and I would agree that Naruto not having parents did lead to some selfishness and self-absorption on Naruto's part that wouldn't have been there otherwise), Sakura simultaneously envies Naruto's freedom, as he is able to do whatever he pleases without having to worry about parents dealing out punishment.

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Sakura's glib approach to what it means to have parents angered Sasuke. Unlike Sakura, Sasuke understands Naruto's pain. Sakura never enjoyed a great relationship with her parents: her parents were at times rude to Sakura and seem disinterested in their daughter for the most part, and Sakura is regularly annoyed by Kizashi and Mebuki. Sasuke, who was on much better terms with his parents and loved his parents more than Sakura did hers, is disgusted with Sakura for not realizing the treasure she has in her parents. He snaps at her for her criticism about their teammate and for her philosophy on parents, telling her that even parents scolding or yelling at you is a joy compared to the empty, miserable loneliness of having no parents at all.

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Sakura was insensitive to Naruto's plight and loneliness, and she was being rude about Naruto's behavior: it's not Naruto's fault he doesn't have parents in his life to offer correctional guidance. Sasuke snapping at her and calling her annoying wasn't exactly friendly, and he could have been gentler to Sakura, but he wasn't out of line. On a team that includes three orphans who were all torn up and traumatized over their parents' deaths, an attitude like Sakura's would inevitably lead to her incensing the other team members at some point or other. By snapping at her and telling her she didn't understand loneliness or what it meant not to have parents, Sasuke was warning Sakura there were certain lines she shouldn't cross over and things that should not be said if the team was ever to work effectively together and get along.

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Sakura was annoying in this scene. Considering how much hate she gets from fans for this part, I don't think any fan would disagree (this scene is without fail at the center of people's reasons why they despise her character). Sakura was immature and rude and Sasuke called her out for it. I don't see why that qualifies as toppling their entire relationships before it even started. Just because she's annoying in one instance doesn't mean she's annoying in every aspect of her character.

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Sasuke calling Sakura annoying to her face certainly wasn't a relationship deal-breaker. Sasuke can recognize that Sakura has faults but still like her; those concepts aren't mutually exclusive (in fact it's what SasuSaku's relationship resides on). Sakura was rude and out of line, and Sasuke got mad at her and snapped at her because of it. It doesn't mean he hates or dislikes her. It just means that occasionally her rudeness goes too far and he's not just going to silently observe. If she rubs him the wrong way, he's going to call her out on it and alert her to where she is irritating him.

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It's not like Sasuke holds this moment against her; never once does it re-emerge in his memories. Seeing as how he opens up to Sakura and sticks by Sakura's side during the bell test even at great detriment to his own goals, it shows Sasuke wasn't deeply bothered by Sakura's thoughtless musings on Naruto, not even short-term. And certainly not long-term.

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Besides, Sasuke criticizing Sakura and telling her she was annoying had a positive effect on Sakura. Because Sakura thought more highly of Sasuke than of other people, she took his opinion more seriously. As a result, Sasuke's words caused Sakura to think introspectively and use empathy to consider Naruto's feelings, probably for the first time in her life.

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Sasuke's words weren't the kindest, but he did provide Sakura with some much-needed criticism, a critique Sakura was able to use constructively because of her respect for Sasuke. This moment caused Sakura to become a far better person: she went from unbearably annoying in the first few episodes to a more tolerable and understanding person who was still annoying at points, but much less so.

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By snapping at her for her rude behavior, Sasuke gave Sakura the opportunity to better herself, let her know where his patience ended, and gave her a warning of what wasn't going to fly on Team 7. Rather than brush off Sasuke's words, Sakura internalized it and considered his words seriously, and used them to better herself, which ultimately resulted in Sakura being a better person and in greater team unity.