I think the biggest problems most people have with Navi are:
1) Her constant cries of "Hey! Listen! Hey! Listen!" when we KNOW what it is we need to do.
Yes, we get it, Navi. We need to go see Saria in the Lost Woods. Kinda busy trying to win Epona here, though.
Yes, Navi, I know we need to find a way to un-freeze Zora's Domain. Just let me figure out how to get this one Heart Piece and then we can go.
I'm not saying she isn't helpful, but with a giant world to explore, as dire as the situation is, one can still make time to stray from the main story for an hour or two to do some exploring.
2) Her stating of the obvious makes players feel like they're playing as an idiot.
Yes, Navi, we see the chest in front of our face. Yes, Navi, we know there's an enemy in front of us.
Of course, then there are also the times when it WOULD have been helpful for her to point something out, but she didn't.
Huh, guess Navi didn't notice the Like-like on the ceiling, either. Huh, guess Navi was so focused on that chest right in front of our face that she didn't see the enemy behind us.
Again, not saying she isn't helpful. The problem is her priorities sometimes need some work.
Do I hate Navi? No. I think she's a wonderful sidekick. She just gets WAY too focused on one thing, to the point that she seems to be obsessed.