Well, this is a problem with using packages from outside the Ubuntu repositories. You will need to either ask the Docker Engine Developers to write an apparmor profile for you or write your own. Same with a selinux profile.
Now here is where you will start to get options, should you use or not use LXC, apparmor, selinux, etc.
For example, the Docker developers feel you need to update - http://blog.docker.com/ and that is certainly one way to manage the situation.
Apparmor and selinux protect you (potentially) from zero day exploits, but exploits are fixed via updates.
The advantage of apparmor is that it is easier to learn. The disadvantage is that you have to write you own profile.
See the apparmor docuemntation
or, for a practical example, using a rather simple program, see http://blog.bodhizazen.net/linux/apparmor-privoxy-profile/
As long as we are on opinions ...
RHEL and Fedora are a bit ahead of the curve compaired to Ubuntu in terms of Virtualization. RHEL is working with Docker to provide support, inculding selinux
I am not sure about Fedora and Docker.
But Fedora uses selinux and virtmanager to manage LXC - http://major.io/2014/04/21/launch-secure-lxc-containers-on-fedora-20-using-selinux-and-svirt/
At the end of the day, you will have to review the opinions and go with the solution that works best for you.