Flying sounds great. In reality, however, you are about to spend time (perhaps, a lot of time) in an extremely unhygienic space.
The most obvious thing is the air that you breathe whilst among the clouds. Funnily enough, air is not a big issue. The air in many aircraft is bled from the engines and compressed by them, this is then mixed in with the air already present. On some newer aircraft, for example the 787, air is drawn in from a separate electric compressor under the aircraft (not because it is better for you, but because it is more fuel efficient). In theory (and really, in practice) aircraft air changes every 4 to 6 minutes which is actually better than some hospital delivery and operating rooms and significantly better than most if not all, office buildings. That said, the air very often goes up front first, (logical, really) so if someone has a bug up front, it may well get to you before it is recycled.
The most unhygienic part of flying is, well, the passengers. Not all of them, true, but many of them. The tendency to dress down and then there's the "I'll have a bath when I get there" approach. This happens a lot, these days and then, to make matters worse, people remove shoes and socks, allow hair to hang over seats, remove tops and even shirts. So, where does all the dirt lurk?
An aircraft has to turn around very quickly so there is not time to give an aircraft the deep clean it should have, each time. Tray tables are a major breeding ground for bugs. A 2007 study found methicillin-resistant Staphylococcus aureus (MRSA) on some 60% of the aircraft tested. The tray table is not wiped down and is used heavily to rest food and drink - and spilt drink and food - to rest books on, various bits of electronic kit, hands, and even heads whilst sleeping.
In 2014 a study was made and found that MRSA and E. coli, can live for a long time in airplane environments. Six types of materials from aircraft (armrest, plastic tray table, metal toilet button, window shade, seat pocket cloth, and leather) were tested by spreading the germs onto each material and then putting the samples into an environmental chamber that mimicked the pressure and humidity of an airplane.The MRSA lasted the longest on the seat-pocket material, surviving for 168 hours, while the E. coli made it 96 hours on the armrest material. (Credit and story here)
Middle seats are the most unhygienic of the three or four abreast seating types. Mainly because, with anyone passing over, these are the seats and seat rests that get touched the most. If someone is ill, then they will spread whatever it is they have, whilst en route to the loo, touching seats all over as they go. Taking some hygienic wipes, therefore, for the tray table, armrest and anything else, is becoming a must, no matter what class you travel.
Airline toilets really are the pits. Whatever you do, never go to the toilet without wearing your shoes. These are cramped spaces, with a small basin which invariably sloshes water everywhere and when that water sloshes, whatever the last person to use the facility washed off their hands, sloshes with it. Remember that any toilet can only be cleaned when the aircraft is on the deck. This means if you are at the end of a 14 hour (or even 6 hour flight) Need I say more?
A lot can be done by passengers to make aircraft generally more hygienic places to be. Granted, that as a coach passenger, you are likely to be confined to a fairly small space for a number of hours. You are not going to wear your best clothes; but this does not mean that clothes cannot be clean. It also does not mean that you can avoid washing, either. You have to share your little space with many others; finding your self sitting with someone who has not washed or brushed their teeth is not pleasant, so if everyone washes and takes a bit of care over their personal hygiene, every trip will be that little bit more comfortable.
Keep your clothes on and you bits of anatomy to yourself. If you do remove your shoes, then make sure you have clean socks. Do not remove socks as firstly, you may love your feet - others will probably not and secondly, remember what I said earlier about pathogens? Exactly. Keep your anatomy to yourself for the same two reasons. It is not pleasant for others but more importantly, if you let hair or naked limbs fly all over the place, they, too are collecting a nice little batch of bugs who can then have a field day on (and in) your body.
Your fellow passengers will thank you for it, your Flight Attendants certainly will and so will your body.