Although it is almost universally hated how she will interrupt you to teach you things like how to open a door (it seems like I complain about this more than anything else)
This is what I hear the most commonly. But then again, I've met people who are not used to the way the game plays. Any game can be tough on your first time, it actually happens toi me all the time. It took me days of playing Super Mario 64 to get the jumping right and it took me about the same time to be good at Ocarina of Time and get used to the controllers. You know why? Because people who are not used to a certain kiind of game take a while to get the gist of it as simple as it might be for the more experienced players. Believe me, I've tried to get many people I know to play Zelda and they always get the simplest things wrong (moving blocks, jumping, using items...you get it), but so did I when I was first playing it, so I can understand that. Maybe it's easier for people who are already used to not having to look at the buttons because maybe we already have the layout in our mind. But my mom, for example, could never get into the console Zelda games because she got fed up with having to look at the controller to see which button she was pressing all the time.
Anyway, before I get off-topic, here's my main point: They had to take that kind of people into account, and that involved making instructions for the simplest things. Let's admit it, not everyone is going to instinctively know how everything works in a game.
Also,
as Thareous said, the first attempt at being a 3D title was sure to be a really new experience to people, so Nintendo had to make sure nobody got "left behind", if you get what I mean. But then again, that does get repetitive on repeated playthroughs, so it's probably justified in that sense. Still, it has a purpose, so I think the help from her is justified there.
Then, there's also this:
Call me weird, but I definitely have a love-hate relationship stance with that fairy. As a character in herself, Navi is just simply adorable and an all-around sweetheart in my mind. On the flipside however, the constant cries of "HEY!" "WATCH OUT!" And the fact that she keeps telling you things you know already can be downright irking! XD; But yet I get sad every time I see her leave Link in the end credits. It's a complicated slew of emotions, really.
I always liked this aspect of how you can take Navi's personality the way you want. I always thought of her like a sister to Link or something along those lines. As it was so vague, there wasn't really any in-game evidence to contradict your view of her. That's the beauty of vague characterization right there, you just have to fill in the blanks.
