Intimidation factor, maybe. You can't see a sub...but there's no mistaking a B-1 flying overhead.
Case in point, check out this B-1B high speed flyby vid from Afghanistan. The concept and image of a supersonic bomber that looks & flies like a huge swept-wing fighter jet is just super cool.
See http://www.youtube.com/watch?v=z0-Ate1eohE&list=PLA94448E7710F5983