Samsung, HTC, Dell, etc... all have other cross cutting businesses that could influence whether they play ball with MS on issues like mobile patents, B&N has no such constraints.
EDIT: In addition the Nook is probably the lone shining star in the B&N business, they can't surrender a single point of margin if they don't have to. If the Nook becomes untenable as a business B&N could become untenable as a business and sooner or later they'll go the way of Borders Books.