I'm sure there is a reason for this move, be it vindictive, the NFL "ban", competitiveness, etc.
But, it could be Apple wanted to make room available to push its own Beats speakers/headphones and told Bose, rather than have 10 items in our stores, we will only carry 2 which ones do you want, and Bose said NONE.
Apple needs space for their Watches later on.
Maybe Apple only wants 10% "hi-end/hi-priced" speakers and Beats fills that entire percentage.
Apple makes money off Cases or cables from third-parties because they use the MFi or whatever license. but for headphones, I'd guess nothing. maybe sound docks they would for the license but when you are selling $100+ headphones, I am sure Apple wants the most $ it can take from it, and Bose headphones won't get them much/if at all.