Everyone knows that girls get germs from boys and boys get germs from girls. If a boy touched a girl, she wouldn't get boy germs if she had 'keys', which simply meant that she had to cross her fingers.
If you got tired of having to keep your fingers crossed, you could 'swallow your keys', by miming sticking your crossed fingers down your throat. This provided germ protection for a considerably longer, although undefined, amount of time.
'Keys' also worked for some things that weren't germ-related. If someone was doing the "I'm crushing your head!" bit with their thumb and index finger, as seen on the TV show Kids in the Hall, you could hold up your crossed fingers and say, "Nuh-uh-uh! I got keys!" This rendered their crushing of your head ineffective, so then you'd probably just punch each other for a while.