Certain animals have been with humans long enough that
it could be said to be their natural environment. Human
parasites (hmm... Stop, doctor! That tapeworm has rights
too!) are the obvious example, but certain furry
animals also fit the mold. Animals that have undergone
evolutionary change that makes them more fit for an
environment as a companion animal can be said to
be in a natural environment when kept as pets; a
similar argument can be extended to some food animals.
Of course, if one accepts that humans have been messing
with nature and that they shouldn't do that, animals that
have adapted to associate with humans are aberrations.
This raises the question of what to do with them, since a
mass liberation (run free, little animals!) is
is condemning those that aren't still suited for
life in the wild and don't go back to their owners
to death. Many of those that are suited for life in the
wild (which may include life as a scavenger on the edge
of human civilization) will have a short, unpleasant
life. Is that worth increased freedom? Does it even give
them increased freedom? It's too bad we can't talk to
the animals to find out.
It could be argued that severely mentally or physically
handicapped humans who are kept in institutions or
homes that they are not able to leave of their own
free will are kept in a state analogous to that of
pets. Just like pets, they're (ideally) fed,
groomed, and otherwise cared for in ways they are
unable or perceived as being unable to care for
themselves. Those who are kept in such facilities but are
able to leave of their own free will could be compared
to outdoor pets.