We've made many trips to WDW. Most, thankfully, we have all remained healthy, besides some colds and minor bugs. Two trips were different, however. When DD was 3, she got Rotavirus and spent 5 days in the hospital and at age 5, she wound up with walking pneumonia.
Sure, WDW is a breeding ground for germs, but so is every other place that attracts large groups of people--especially people from all different areas. Think about it--when you hold the lap bar on Peter Pan, how many other people touched that today. You could ask the same of every surface at WDW--or the mall, stadium, school, airport... I've seen kids sticking the queue chains in their mouths! The list of possible germ transmittal surfaces is endless.
That being said, a little common sense goes a long way and everybody needs to decide what works best for their families. I'll admit to some OCD tendencies. I don't like staying in hotel rooms at all. I bring my Lysol, bleach and Clorox wipes everytime. Does my spraying and cleaning really make a dramatic difference in the germ count? I have no idea, but it makes me feel better.
I carry anti-bacterial gel and have no qualms about using it--often. Our skin's primary purpose is to be a barrier against germs and other invaders. Putting scented alcohol (which is what those gels are) on your skins is simply topically cleaning it. Alcohol kills bacteria, just like soap. Your skin does not build up any sort of immunity to soap or anti-bacterial gels. (If it did, hospitals would not have anti-bacterial gel dispensers located every ten feet down every corridor with signs recommending visitors use the gel before and after visiting a patient.)
We also wash our hands every time we visit the restroom and before we eat anything. I also discourage DD from putting her hands near her face, especially her mouth. I do this everywhere, but am a little extra vigilant somewhere like WDW.
I case the point of this long post is simply to say that germs are everywhere and each person needs to decide what steps they want to take to stay healthy. It's the same with many choices in life.
Here's to good health for all--especially at WDW!