The main reason many cameras do not have 100% viewfinders is the same reason that they don't all have full frame sensors, huge buffers, and GPS embedded. The same reason that all lenses are not perfect glass, IS, and f/1.0 : cost.
It's all a trade-off. Every camera can have 100% viewfinder, but it might have to give up a feature, or increase the price. This is why the Canon 1D/1Ds, and nikon D3x/s are so expensive: they have no or few compromises.
Edit for coneslayer comments above...I think it reads easier here:
I will amend this response to add that part of the manufactures decision is not only cost but perceived cost and value. Manufacturers of all goods seek to differentiate their offerings and camera vendors do so by offering different features and benefits. We know that nearly all Canon cameras now have the same basic chips inside, but some cameras claim to have more buffer size, etc. It is also just as likely that some simply have different software loads on the same chip, thus reducing parts costs while offering different features via software. Viewfinder view could be one of these differentiators as well, and at least with Nikon and Canon, we see 100% viewfinders on their top end cameras ($5000+), but often not on beginner models. This suggests that its either a differentiator or a cost factor.
Another possible reason is the following: if a manufacturer promises a 100% viewfinder, this suggests a level of precision that is not in a 96% viewfinder. 100% is just that: it must match the exact view that is seen by the sensor. If the prism or mirror or anything in the view path is slightly out of alignment, the photographer may assume something is in the shot that actually isn't. Imagine your surprise if your shot is different and does not include the subject as you saw in the viewfinder. On the other hand, if its a 96% viewfinder, your view will be smaller than the sensor view, and the final shot will include portions of the subject NOT in the viewfinder, giving you ample margin to adjust your image in post as you see fit. With 100%, there is no margin.
I have to assume that the precision to deliver 100% vs 96% is significantly higher here, and more importantly, much higher cost. Alignment issues on an automated line could mean costly scrapping of expensive parts, and hand assembly I would imagine is too costly for volumes needed for Canon xxxxD/xxxD models.
I suppose a vendor could also provide 110%, and draw a box on the viewfinder around the assumed sensor view...but I don't think I have seen this since old rangefinders.