Our daughter with CF is 10 months old. We were already giving her physio without realising it before her diagnosis at 9 weeks old- because she liked to be 'patted' heavily to sleep! Sometimes she likes it, sometimes she'd rather play, but we just persevere and try and distract her until it's done. She has the DDF508 mutation and pancreatic insufficient. She got a viral infection at 5 weeks old and has basically been intermittently coughing and wheezing ever since.
I have stayed in the hospital with her on 3 occasions now, the first time for 5 days, the second was for 5 weeks (she was 5 months old) and the third time we are nearly at 3 weeks, and still here- but we should be going home soon.
I questioned everything in the beginning, all the meds and treatments and the approach, but after a while I have come to know the staff and the medications and know better who and what to trust and what approach works best for her. She has allergies too, so I have to be knowledgeable about how they affect her wheeze and digestion because many of the respiratory doctors don't seem to know that much about that side of things. It's a steep learning curve!
I remember it all being very difficult and stressful in the beginning, but you do get the hang of it all. I think that babies and children are much more resilient than we realise.
As for the germ thing- I felt very in the dark about what the best approach was. Our CF specialist paediatrician said that general cleaning is sufficient, that the kind of bacteria that cause problems can be found anywhere and it is impossible to eliminate them all. Pseudomonas can be found on clean/sanitised hospital surfaces, and I wonder if in trying to always get rid of them we actually encourage the re-growth of more persistent strains. As you would know- babies go through a phase of putting everything in their mouths and you would go crazy trying to prevent this from happening. Their stomachs can cope with just about anything, so worry less about that (and it is good for their immune system to 'taste' everything). If you want to be careful, it's more about what they breath in, and it is my understanding that there is heavier bacteria growth in things like stagnant water, compost and piles of lawn clippings, and dirt. The other thing to be careful of is respiratory infection so it's important to try and avoid people with coughs and colds- train your friends early on this one to keep away if they are ill!
The kids need to have a life, so eventually you will find a balance between being careful and still having fun.