They can be. You need to research the ingredients and figure out whether it's bird safe or not. Many birds are particularly sensitive to air contaminants.
Fly control is pretty simple (unless you're talking about the biting/blood sucking variety); keep everything clean and dry.
Mosquitoes are a bit tougher because they're attracted by warmth and carbon dioxide (from exhalation). Some species are also attracted to light. It's hard to teach your chickens to be cold and hold their breath. 
MOST mosquitoes attack at night and the rest will tend to make their daylight strikes in cooler, shady areas. Other than keeping your birds in the sun all day, there's little you can do during daylight. However, if they've got a coop that they're in at night, there's no reason you can install regular bug screen (just like what's in your home windows) over vents to keep the little blood suckers out and give your chickens peace while they sleep.
