You don't have to listen to Navi. I simply ignore her most of the times. Yes I think she is very annoying but she is also cute.
The biggest problem I had with Navi was that she interrupted at the most annoying of times. Like for example, I'm just about to go to the Fire Temple. I warp into the crater, Navi hasn't said a word yet. I want to look around a little first so I do up C to go into first person view. Right before I press up, Navi decides to annoy me by speaking up at that exact moment.
Navi: "Let's go check that ominous cloud over Death Mountain!"
Me: "What do you think I'm doing in the Death Mountain Crater you blind flying ball of sparkles?!"
I can't help but marvel at her obliviousness sometimes.