Don't read this USA Today article unless you want to purchase a Germ Free Bee now. Journalistic hero Everett Potter debunks several myths about air travel, INCLUDING the misnomer that airlines have a motivation to clean the plane between connections.
The FAA doesn't regulate or inspect aircraft cleaning, so frequency and thoroughness are left up to the airlines themselves. Gobbels of MedJet Assist says that as a rule of thumb, an aircraft is supposed to be completely wiped down after every 30 days of service or at 100 flying-hour intervals. But in theory, that means that an aircraft can be used for dozens of flights between deep cleanings.
Airlines are notorious for cutting corners to save cash. We'll presume paying a crew to deep clean your plane seat is one of those corners.
The chair upholstery is an especial concern.
From Potter's article:
The real problems lie on the chair upholstery, the tray table, the armrests and the toilet handle, where bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and E. coli can live for up to a week on airplanes that aren't properly cleaned.
A Germ Free won't protect you from every sneeze and cough on that cross-country trip. But a high quality airline seat cover will definitely help create that first line of defense. Airlines have become veritable refugee camps, people. Fight back with a Germ Free Bee.