Eventually docker-machine will deprecate boot2docker-cli (the piece which you use to actually manage the VM). However, boot2docker-cli is (mostly) pretty stable and a lot of people use it (including me), so we don't want to toss it out overnight or without a good migration path for b2d users.
boot2docker sets up a virtual machine with docker. Machine does this too, but it also allows you to choose a cloud provider, instead of only your local machine.