Running untrusted programs as root in a docker container is definitely not recommended (and indeed you should be very wary of running anything as root). In the slides, I didn't have time to go into how to run processes in containers without root privileges, but docker does provide features for doing so, and it's definitely worth using them.
Would you please consider modifying or extending this presentation to include other basics? You did a great job at making Docker finally understandable as a whole. I'd love to see more of your writing on this topic.
Thanks! I will see what I can do to add more. Note that the source for the slides is on github [1], so anyone who'd like to pitch in can do so, and that would be most welcome.