I've finally come to the conclusion that WDW is probably one of the most germ-infested places on the planet. I mean, when you think about it, who wants to ruin their time at WDW by canceling due to sickness, or even spending a few days in their hotel room because they don't feel well.
It isn't just WDW. I go to a lot of Science Fiction Conventions and getting sick afterwards is so common most people expect to come down with "Con Crud", even though we don't have germy guard rails or ride cars. It's just a consequence of overstressed bodies, irregular habits, and lots of people in close quarters.
If you think about it, your immune system is probably stressed to begin with due to pushing your body to its physical limits with the addtional walking, lack of sleep, irregular meals (mostly fast-food type), lots of excitement (excitement and adreniline from thrill rides take their toll on your body too) etc. Then add in that you are cheek-to-jowl in lines and crowds with tons of people from all over the world, each carrying a normal complement of bacteria and viruses that they may have a tolerance for but you don't. So it's not at all unexpected to get sick when you get home.
There's not a lot you can do. You can spend a lot of time trying to de-germify your environment, but actually studies show that can lead stronger germs and a weaker immune system. Besides a lot of this stuff is air borne as well. You take reasonable precautions, you try to take care of your body (without losing too much park time), and if you get sick after, you just have to deal with it as part of the price of the parks.