It makes sense. The Red Sox had a glut of starting pitchers -- Schilling, Beckett, Wakefield, Clement, Wells, Arroyo, and Papelbon.
Nixon is getting old (turning 32 on April 11th) and he will be a free agent after this season. Pena will be the Red Sox future starting right fielder. They will likely platoon Nixon and Pena in RF for now and may even try to trade Nixon sooner or later.