Zeiss recently introduced autofocus lenses for the Sony NEX (E-mount) and Fujifilm X (XF mount) cameras. Why is that we still only have manual focus Zeiss lenses in the Nikon (and Canon) world?
Simple answer: manufacturer cooperation.
As far as I know, we currently have only four truly documented and open-to-third party lens mounts: m4/3, NEX, XF, and Pentax K. And I'm not entirely sure how open-to-competitors the K mount is these days now that Ricoh owns and modifies it.
Basically, Nikon is a closed system. For the most part, if you want make compatible lenses for the F-mount, you have to reverse engineer the mount (and there are an incredible number of subtle changes that have occurred to signals on that mount over the years as cameras and Nikon's own lens technology changed). Rumors abound that Tamron has gotten some inside help with the F mount, apparently due to licensing lens designs and doing some manufacturing for Nikon. Tokina was formed by ex-Nikon engineers. Sigma took the total reverse engineering approach and sometimes gets burned by it (a lot of their lenses have needed firmware updates when new cameras come out).
If you're a relatively small, more niche type manufacturer such as Zeiss, it's easier to proceed if you have full cooperation than if you have none. Your resources are more focused on the things that make you unique, not figuring out what the camera maker is doing. You're niche to start with, so you're not looking for huge numbers of lenses to be sold, either. Thus, mounts where lens choice is low but camera quality is high are highly inticing to such companies.
The risk to Nikon is that as other mounts attract more and more third-party options, especially quality ones, those mounts themselves become more enticing and start to propel camera sales. I've written about this before: the perceived sum of the parts in a true system exceeds the factual sum of the parts once you get past a certain bar. m4/3 is already there. NEX and XF are trying to get there.
Nikon's real problem is simple: the only "mount" they seem to be protecting is the FX version of the F mount. DX is a panoply of mostly kit lenses that come with cameras. CX is another go-it-alone attempt by Nikon with minimal offerings.
As compact cameras go away as viable sales builders, camera makers like Nikon are left with only their systems to pull in the majority of the cash. Why Nikon isn't trying to make CX and DX the most viable systems I don't know. FX by itself isn't going to bring home the bacon for Nikon.
So the unasked question is this: when will Nikon either step up and truly fill out their CX and DX lens lineups, or when will they encourage others to do so? So far, the answer seems to be "never" for DX and "we're slowly working on that" for CX. Wrong answers.