The most important thing that you can do is to be in the best health that you can be in. If your immune system is compromised or you are very susceptible to germs, there are masks that have been designed to filter the air for you. This is an extreme measure and one that everyone doesn't need to use. Many aircraft use a HEPA filtration system designed to remove most of the particles from the air before it is sent back into the plane. Get plenty of rest before your flight so that your normal immune reactions are up to par. You may want to take a round of immune boosting vitamins for a week or so before your flight.
The air in airplane cabins is very dry. Most of the moisture is removed from it to help to keep the cabin cool. You can fight this in two ways. Use a saline nose spray to keep your nasal passages moist and make sure that you drink water before and during your flight. That, of course, is a double-edged sword, if you drink a lot you need to use the restroom a lot and they are filled with germs from the water to the handles, they are just everywhere.
Carry jell disinfectant and towelettes (make sure it is small enough to pass through the TSA
Stay away from any drinks with caffeine which is dehydrating and also avoid sugar. You may want to suck on a sugar-free candy to help keep your throat moist. There are some products that tout themselves as helping to protect you from airborne germs but there is no definitive proof that they offer any help keeping healthy during and after a flight.
The pillow and blanket that the airline provides do not get cleaned frequently enough. If you are healthy, this isn't an issue and being cold during the flight is a bigger risk but, if you are able, carry your own pillow and blanket. The tray and the armrests also will hold germs and your best defense is just to wipe them down yourself and then wash your hands as often as is reasonable.
Keep your hands away from your face, this will keep the germs away from openings where they can get into your system. Bring your own reading material, the ones that are on the plane have been handled by everyone who has been on that plane before you.
At the end of the day, government studies have shown that it is no more dangerous to fly in an airplane than it is to work in an office when it comes to airborne germs. Your chances of catching something from another passenger or your fellow worker are both about 1 in a thousand. Go ahead and enjoy your flight, practicing your normal everyday precautions will help you to avoid anything unusual you come into contact with.
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