Should I dockerize different servers running on a single machine?
Yes, Docker prefers "one process per container" approach. I would not see this as an overkill, quite to the contrary - at your case it might rather soon be beneficial to have instances of different users better isolated: less security risks, easier to maintain - say you need new version of everything for new version of you app, but would like to keep some of the users still on an old version due to a blocker.
I want to make simple service that each user will have his own (simple and light) webserver. 
I want to use an AWS instance to do this.
I understand that I can do that by starting Python's SimpleHTTPserver (Proof of concept) multiple times on different ports, and that the number of servers I can have depends on the resources. 
My question is:
Is it a better practice or an overkill to Dockerize each user with his server ?