Too expensive to make, too faffy to use and not enough obvious applications. OK, so you can view 3D movies on it. There are maybe half a dozen in existence (if you don't include 1950's B movies and the like) and actually not that many more currently in production. And frankly while the TV makers may bang on about it all they like, there doesn't actually seem to be any great consumer demand for 3D displays. And after movies, what else can it be used for? It doesn't help or hinder other media and it's application in text based applications like the web and email is minimal. You could define a GUI that allowed windows to be stacked in 3D but that's functionally no different to windows being stacked in 2D.
Apple isn't in the business of selling niche products to markets that don't exist yet. It's in the business of taking an existing market which it considers moribund and applying technology to it in innovative ways to more easily solve the problems that already exist. Apple isn't about doing 'new', it's about doing 'old, better'.
The tablet will not be a device that specialises in showing you media that you don't have yet. It will be a device that allows you to access existing media in a more functional, ergonomic way. It's much more likely to be the device that wipes out the netbook than it is the device that kickstarts 3D.
Jon