Germs?
BUT you're in close contact with a lot of people, some of whom are carrying germs from different locations. Stuff you've not been exposed to so you don't have a resistance to it. I always picture it kind of like if you were stuck in a really big elevator for a few hours LOL.
I don't think it's too much different than, say, taking a train somewhere for a few hours though. I will say I kind of like flying in the little puddle jumpers where the cabin layout is two seats, aisle, then a single seat... I like to snag a single seat so I'm not sitting next to anybody!