@Charagon:
Generally it's because they interact with each other on a far more regular basis than most of the crew. They frequently pair with each other when the fighting starts as well.
As First Mate and Navigator, they're the ones in command of the crew when Luffy is away/distracted. They are the only ones, other than Luffy, that can order each other around. There's also the constant bickering, note that they are the only two members of the crew of opposite sex that actively bicker with each other on a regular basis. The only other pair is Zoro and Sanji, and DeviantArt is way too into that already so I'm stopping there.
From a sheer storytelling standpoint, it'd be a great end to have Zoro, who's generally uninterested in women, hook up with the girl that his rival Sanji, who is very interested in woman, joined the crew for.
Finally, he's got the world's worst sense of direction. Who better a pair than him and the world's greatest navigator?
And if you want a really really REALLY weak rationalization…. in the last two openings of One Piece Nami turns her head to look at Zoro when she has her pick of the whole crew to focus her attention to.
Meh Zoro hardly if ever takes charge though. Nami usually is the one to do that and that's because she's probably the smartest one there along with the one who has the most common sense. Outside of Robin and maybe Usopp.
and it's probably just coincidence that they pair up when the fighting starts, and to me it just always seemed like the bickering was good comic relief.
and well let's face it I don't see how ZoNa is Zoro getting one up on Sanji either since Sanji basically has feelings for anyone with boobs and a vagina. So if anything he'd just move on to Robin or whatever other girl he see's.
As for the last point you could say that about LuNa too since Luffy has no sense of direction and needs Nami far more than Zoro does.
Not trying ot get into a pairing debate or anything. I don't want it to seem like that. I just think it's more of an exchange of ideas.