I can only relate to my experiences & taking sick kids on planes.
As for my family, my son does get sick alot. Test have been ran on him to see why he gets sick so often, every test has come back normal, including things like cancer & other serious illnesses.
So most of the time when my son gets sick I know it is just a cold/virus/flu. What is weird is NO one else in the whole family catches whatever my son has.
Before our trip when my son first came down with symptoms, I took him to the doctor to get him checked. I mentioned we were going on a plane the next day & they said to continue with our plans. That he probably just has a common cold/virus.
As for the plane ride itself. He slept 99% of the time & I had him covered up & tried to aviod people. The "good thing" was at this time he had not developed a cough yet so he wasn't coughing out germs.
I am big on handwashing, cleaning the house, etc. My son still gets sick. We (I & his doctor) are hoping he out grows this getting sick all the time but only time will tell.
Once we got down to Disney we do not go into any parks until his fever was gone. Btw--no one else on the trip got sick.
So in our situtation my son being sick is a common problem in our house. We have learn to deal with it. I DID go back & forth about should we go on the plane or not. When we were leaving he wasn't THAT sick. His temp was only 100-101F, gave him some Mortin & THOUGHT he would be OK. It was not until we got down to Atlanta at our transfer that his temp was up to 103F, (of course gave him some Mortin) & it wasn't until we got to our room his temp was 105F.
Also, as soon as we got in our room I called the front desk to see where the nearest hospital was, they told me they will send the EMTs right away. They started with us until my son's fever was down to 102F. We then left to go to the local clinic, which we were told "it was just vuris" since his strep test was negative, his lungs/chest was clear and everything else seemed OK.
The only way I can keep my son from getting sick is to make him live in a bubble. That is not an option.