Actually, Bruce, the pilot isn't necessarily at the controls the entire time the plane is in the air. Not to say the cockpit is empty at any given time. But most modern airliners have autopilot and don't require the entire flight crew to be in the cockpit. In fact, I believe several more sophisticated airliners can land themselves (via computer). So the flight crew can leave the cockpit in shifts on longer flights, nap, eat, go to the bathroom, etc.
Contributing to the subject at hand...I've heard the flight crew is given the best of the best from the First Class and Business Class meal selection, although they may choose to bring along their own food. The primary concern of the pilot and first officer eating different entrees probably has to do with food poisoning - if one entree is contaminated, the other is not, so if one crew member is incapacitated, there is still someone to fly the plane.