The people in the world who seem to know something bad is about to happen seem to be Zelda, Impa, the Deku Tree, Navi, and Link. Some of them have to be told by the others, but they all believe in Link's quest in some way. Other people seem to know that there's something bad with Ganondorf, but she is a member of that core group that I think realizes exactly how bad things could get. She gets points just for that. She is also protective of Link, judging by when she's shouting at him to "Watch out!" and warning him about hot lava (which you think would be a no-brainer, but the point is that she's looking out for him.)
And I've mentioned elsewhere, but I really love her line at the end of the game that, "There's no way he's going to hold me back again! This time, we fight together!" And this is after Ganondorf has survived the destruction of his tower and transformed into beast Ganon, which is one of the only times I think he's truly scary. Teeny tiny fairy Navi, willing to go up against one of the greatest evils in Hyrule's history. I love her just for that.