Here a link describing a the background of the controversy.
As Nate points out PETA believes that it would be better that pets had never existed, since they believe pet-owning is selfish and causes pain and suffering for the animals. But they also say that it is a myth they are trying to "free all the pets."
Contrary to myth, PETA does not want to confiscate animals who are well cared for and “set them free.” What we want is for the population of dogs and cats to be reduced through spaying and neutering and for people to adopt animals (preferably two so that they can keep each other company when their human companions aren’t home) from pounds or animal shelters—never from pet shops or breeders—thereby reducing suffering in the world.
Read more: http://www.peta.org/about-peta/why-peta/pets/#ixzz2zqRx25O0
Domesticated pets that were freed would be more likely to be injured and get sick, so it is a "least-worst" option. They have many campaigns targeting improving the lives of pets. I believe that since snakes are wild animals, they see a difference.
The Humane Society of the US does not seem to have a secret anti-pet agenda. The issue is that they are running a manipulative pro-pet fundraising campaign, when the national organization hasn't run a pound since the 1970s, and its funneling all but 1% of the funds to other lobbying efforts. They also have close ties to PETA, who while not fond of pets in theory, are not seeking to abolish the institution.