I am certainly not an expert on this, so I am speculating to stimulate discussion.

I believe I did read that NW and Midwest Express are ending their relationship because it was lopsided for one party. My guess is that airlines like to "net" out these deals, meaning they expect close to the same number of their miles used on the other airline as the other airlines are used on them. I would assume there is some sort of cost attached to the airline who has more of their miles used on the partner, but I would suspect the difference in miles is often low.

Now on the other hand, non-airline partners buy miles in large quantities and get good deals, this is a major money maker for the airlines. I agree with the previous post that FF flyer programs have turned from loyalty programs to markieting programs, at least until you hit elite status.