Actually they can get them from being in the weather. If there's a drastic change in weather, particularly if accompanied by wet weather, they can take to being sick from the lowering of their immune system.
They also can get respiratory illnesses very very easily from mildew and stagnant air. Ammonia from chicken droppings can very easily cause this.
Another cause, vitamin deficiencies. Vitamin A deficiency mimicks respiratory disease but is actually a non-contagious condition that, once it lowers the immune system, can cause the bird to be more susceptible to actual contagious diseases (or latent disease within that bird itself - relapses).
And as if that weren't enough - viral and bacterial diseases are spread by feather dander, droplets in the air, wild birds, environment, etc.
Your best bet with your babies are the following:
Lots of very very fresh completely fortified age-appropriate feed. Smell the bag when you open it - it should smell strong, not like cardboard. The bag should not be dusty, and it should have been kept in cool conditions. When you open it, you store it in a cool dark air-tight container and use within the month. This helps keep vitamins (like vitamin A) from degrading as quickly.
Lots of fresh air and sunshine! Sunshine is actually a disinfectant, and fresh air is absolutely necessary for birds. (Remember the canary in the coal-mine. They're SO much more sensitive to everything in the air.)
Dry but not dusty environment. Dust is as harmful as mildew - so strike a balance. For shavings, I like to put mine in a box and shake first (out of the coop) then scoop the shavings off of the top as the dust settles to the bottom of the box.
Using VetRx occassionally doesn't prevent illness, but I feel that keeping the nares clean with it in dusty conditions really does help them just as Vicks helps humans.
Clean fresh water - few additives unless needed. The only exception I make (unless treating a bird) is organic apple cider vinegar occasionally. But I don't do it every day and rarely even do it weekly unless I'm doing something specific.
Quarantine all new birds (both for the sake of the new bird as well as your own flock) for no less than one month. Always.
Check your birds weekly. Look at each one carefully. Pick them up for a thorough exam no less than monthly, especially their weight, etc.
Also - don't worry.
We all made mistakes AND we all still do. All of us do! Just some don't admit it.
(p.s. hugs to ddawn! )