for me, using docker on my own workstation (OSX) makes it easy for me to test deploy's to multiple machines quickly (even if these are only locally hosted VMs). docker-machine facilitates that by allowing you to quickly spin up and spin down virtual machines locally or in the cloud.
I can see advantages for running docker as a way of streamlining dev environments, and keeping them consistent across team members, but by automagicaly awaying the docker-machine env commands you have effectively lost the most powerful facet of container technology.
Perhaps we would all do better if Docker's toolset docs were written in a way to communicate these design decisions (their purpose, and how they conceptually work behind the scenes)...