I am concerned about flying. I really think you have a greater chance at catching something on the plane. Planes are disgusting. Seriously. At Disney there is fresh air and lots of opportunities for hand washing. We've been lucky at WDW so far, but we've never flown during cold and flu season before. Hopefully her immune system is tough after 3 years at school!
Air filtration systems in planes are actually quite powerful...that said, plane surfaces (chairs, seats, etc) are possibly (not always) disgusting. So, breathing in airplane air is less of a concern than touching a plane surface and then putting into mouth/nose. Bathrooms grow to be disgusting as well; the longer the flight, the dirtier. So go at the airport and then if necessary; early in the flight.
Further, some people are inconsiderate slobs who sneeze or cough with absolutely horrendous attention to prevention. Stay away from them. It's another reason we pay extra for prime seating.
Technically speaking, though, you statistically have a much higher probability catching a virus/disease in a theme park than plane...it's simply a matter of volume of people, nothing more than that. Plane has 150-300 people; park has 10,000 - 50,000. No comparison.
Finally, time in school and/or daycare or sickness as a baby, etc is not necessarily a boost in immunity to a virus (flu possibly yes)...but there are literally hundreds of variations of viruses (cold alone), so for example, a flu once you get a certain flu, you will likely not get it again...but for a viral infection, the variation is it's own code, and so you'll likely get the cold or virus because it's its own beast and then 3 to 12 months later, another cold or virus just like the one 3 months ago and it will/may feel the same, but it is its own unique infrastructure.. in fact there are so many viral cold variations, among other viruses, that it could take decades to build up immune systems to avoid all know cold viruses.
Immune build up is dependent on exposure - the more exposures earlier on, the less likely you'll get sick from it again or if something has a variation of the base code if you will of another virus, but many viral infections like E68 is it's own code and so a child's overall health, rest, diet, prevention, etc, will have a much greater influence on combating it than previous exposures to other illnesses at a younger age . . .in fact I suspect based on the evidence exposure to other illness will have little to no impact on avoiding E68.
So again, know your family/kids reaction to viruses and take proactive steps to avoid or prevent.
Hope that helps a little bit more in thinking about prevention.