Actually, many feral cat colonies are trapped and killed too. Our previous house was on the shores of San Francisco Bay in Redwood City, and there is an endangered sea bird that lives there called a Clapper Rail. The federal government decided that predators were taking out too many of the babies, so they decided to trap and kill all the predators in the general area, including feral cats, raccoons and skunks. There was a big fight about it and then we moved; I don’t know what the resolution was, but their intent was to kill everything.
There are rescues out there that help with the capture of the ferals, spay/neuter the cats, and then either adopt them out to farmers/ranchers as mousers or release them in the wild in special reserves set aside for feral cats. Cats born feral do not deal well with humans and cannot be socialized unless taken in as kittens. Town Cats is a local Bay Area rescue that does some of this, you can read about it here: http://www.towncats.org/feral/feralcats1.html
At The Rabbit Haven, we just took in 19 rabbits from one backyard. Animal control was going to kill them all, so we helped them catch the buns and are trying to socialize them. We already lost one entire litter because the mom was underfed and already pregnant again by the time we got her. The four adult males that we caught are petrified of humans and it is unclear if they will socialize or have to be sent to a sanctuary to live as outdoor feral buns in a protected environment. You can read the story in a local newspaper here: http://www.santacruzsentinel.com/archive/2007/April/14/local/stories/06local.htm
or on our website here: http://www.therabbithaven.org/emerald_rescue_041307.html