It means wash your hands to remove germs. It can also mean being careful not to bring anything from one group of chickens to another. For example you visit your friend and wander round their coop then go home and walk in the same shoes in your coop. Then you find out she is having birds die from a disease which you may have transferred to your chooks from the dirt on your shoes or the germs on your hands. When they say coop hygiene often that just means keeping poop cleaned up so it doesn't get stinky and there is less chance of anything bad breeding in all the old poop.
