From what others have said (very interesting answers and comments!), we could infer coverage percentage is really related to cost, while viewfinder size is mainly related to other factors, i.e. 

 - people who buy low-end SLRs are most likely to
   expect a smaller and
   lighter camera; a bigger viewfinder
   needs a bigger, heavier body like
   those needed for professional gear, that starts to take money.
   But the cost of making just some parts (of the
   viewfinder) *millimeters* bigger is not
   likely to be relevant.

 - market segmentation strategies, as
   cmason pointed out. Coneslayer said
   cmason's point was weak in that he
   "compared it to features that really
   do have a substantial cost of
   implementation". IMHO it's quite
   clear that manufacturers
   differentiate their products with
   both actually expensive features and
   things that wouldn't cost them a
   penny, e.g. some features in
   firmware: in a low-end SLR you can,
   say, assign three functions to a
   button, in a camera which has double
   the price those functions are maybe
   ten or nearly any function available in the
   menu. 
   
   A bigger viewfinder is really useful, but 100% coverage compared to 96% or the like is just one more selling point to please professionals and amateurs who, for different reason and with different expectations, still both of them expecting high standards in every part of their gear, spend thousands $/€ on a top level camera body. 

Well, this is not a real answer, just wanted to let out some thoughts I came up with reading other entries, and to respond to some of what others said. Nevertheless I think my post tackles the "why?" part of the question, so it's not entirely off topic.