The simple answer is that the price of skilled labor continues to increase. And very generally speaking, cameras are made by machines and the L lens are made (assembled) by hand.

Here is how they make them:

Material preparation: http://www.youtube.com/watch?v=OkWsk9rXpcU

Making the glass: http://www.youtube.com/watch?v=7T7BDeMU_Ks

Hand assembly: http://www.youtube.com/watch?v=KpkAWZTwqI4

Also, with the camera bodies, there is an economy of scale that you get making a million bodies versus making a specific L lens that might sell tens of thousands.