Naruto knows that he's not a genius for nearly seven years straight, if only subconsciously. It is quite evident when he first enters the academy and is the only person who can't read or write in his class.
He himself isn't even necessarily consciously aware that it is an issue. But there was an undeniable sense of shame and envy and jealousy and all sorts of other mixed emotions that caused him to go to his 'grandfather' to get him to teach him. Hiruzen does his best to accommodate the boy for what it's worth. But even if there are numerous shinobi within Konoha's ranks, it is hard to justify having one tutor Naruto on basic reading. So, he does his best to find a civilian tutor to do so and he even succeeds.
The tutor he finds is less prejudiced than his peers and never actively attempts to teach Naruto incorrectly, but prejudice is still prejudice, and the tutor is short with the boy.
Children, now, exist in an odd state. They are entirely human and should be treated as such, but also ignorant in a way. Blind, however, they are not. They can even be oddly perceptive. This is such for normal children, let alone one primed to expect people to dislike them. Naruto is, of course, aware of his teacher's prejudice, even if he does not know the source. Just like he is aware of the broader status he holds within the village.
All he knows is that people don't like him. And he very truly does know it. Still, for the first few lessons, the boy does his best to work past it. To do his best to learn to read. To simply do his best to have his new teacher look at him with different eyes. It does not go well. As was already mentioned, due to prejudice, the tutor is short with the boy. They are not as patient as they would be with other children and don't even really want to teach young Naruto. The tutor is headstrong, unwilling to adapt in ways that might help the child and demands that the boy instead conform completely to him and his needs.
The result is that within a few sessions, Naruto begins to push back. It starts small, such as intentionally moving slowly, a painful act that harms himself as much as it does the tutor by prolonging the sessions and thus the time spent together. Eventually, in a particularly bad mood, the boy skips a session.
Unfortunately for Naruto however, the tutor, already frustrated with his student and the slow alienation he feels from his peers, uses this as an excuse to cancel the sessions with the Hokage. The entire scenario ultimately sours any good will that Naruto has towards academics and is one of the original causes for his poor performance in the Academy.
Later, it becomes a source of embarrassment for him, and slowly but steadily causes him to react both more strongly and gently to the scenario. Gently, because he learns how to brush off most initial questions and change topics. Strongly, because when he fails to gently handle the situation, he reacts by completely ejecting himself from the conversations.
It isn't until he is in the middle of his training trip with Jiraiya that this begins to change. The cause is that elder shinobi asks him to be his proofreader for his new book. Naruto can't quite help but react as he has learned and does his best to get out of it. It ultimately causes an intense argument between the two that ends with Naruto exploding while exposing his lack of literacy.
The next day the toad sage quietly but firmly starts teaching him from the beginning, covering content from reading, writing, and history to arithmetic and philosophy. It would also be the day that he starts moving from a lazy and perverted sensei within his pupil's eyes, to what can only be described as a father.
When the trip is over, Naruto, ultimately, did not have much time to work on the shinobi arts, but neither he nor Jiraiya are disappointed with what they have accomplished.
A 'cute' idea that I was originally using in a different story, in the twenty truths format. But upon review, the premise didn't quite fit with it though, nor do I even think it would fit with any other larger story. The logic of canon breaks down pretty quickly if Naruto can't read (from the very beginning to be honest), but as a little one shot, I think it's great.