Let's just go ahead and say this straight up: in this book, birds represent freedom. Is it a coincidence that a book called Freedom is based around a small blue bird that migrates between North and South America? No, it doesn't seem to be a coincidence at all.
Franzen addresses this most directly in the book's final section, "Canterbridge Estates Lake." The birds that have long thrived in the area (i.e., around The Lake Formerly Known As Nameless Lake), and that Walter has loved watching since he was a teenager, are now being slaughtered by the cats belonging to Walter's new neighbors.
He tries doing something about the threat, and encourages his neighbors to keep their cats inside, and distributes "bibs" for the cats that hinder their ability to hunt (making him look all the crazier, but whatever). But nothing works.
Finally, when Walter and Patty move out, they donate their land to a local land trust, to become a bird sanctuary. In other words, these birds have always been free, but this area's no longer safe for them. They literally have to be kept in a big cage, to protect them from the new threats they face. Is this an endorsement of the Patriot Act's restriction of civil liberties? Or a call for greater awareness of the damage wasteful modern lifestyles are having on the planet? Maybe both? Or maybe not.