pilots have language in their contracts that entitles them to specific seating when flying, in uniform, on company business. as others have stated, the pilots union isn't completely happy right now, and so i imagine they'll be less flexible about these provisions than in the past.
they're also humans, remember. they don't like the middle seat as much as you, and they probably have to turn right back around and fly that plane back when they get where they are going.