I don't think you are over-reacting. I would not want my CF child to be sharing anyone's cup. In my opinion, it is just one of those common sense things, like washing your hands before eating, that can cut down on sicknesses. There is no reason to use the saying "kids will be kids"...healthy kids shouldn't share cups either, it's gross!
Most of the time, I run into people who are too lazy/unmotivated to correct the situation, and they resort to saying that I am too germ-a-phobic, strict, mean, over-protective, etc. I have had family criticize me and belittle me, when they are the ones who are wrong. I always have to watch for people trying to feed my son with their bare hands. Yuck! (I know they haven't washed their hands.)
A good gauge would be asking yourself...If my child were healthy (no CF) would I allow him to do this? I would not allow my child to use other people's cups or utensils, eat without washing hands, eat food that other people have touched with dirty hands, wipe butt and not wash hands, ride in car without car seat/seat belt, etc. Just because they are kids doesn't mean they have to be slobs!
A side story: Every time I go to the doctor, I always see a kid in their pajamas. And the pajamas are always filthy, faded, stained, ugly. Why would you not put a clean outfit on your kid before taking them to the doctor? I'm not talking about the latest designer fashions, just something clean and decent! Would they, as adults, go anywhere in public in stained pajamas? No. So why make your kids do that?
So I guess each family has their own standard of cleanliness. I don't feel like I am "keeping my kid in a bubble" just because I have some basic rules to follow. As long as you are still doing age-appropriate activities, like lessons, play groups, or family events, and not keeping your kid locked up at home all the time, you are doing fine.