Run the script secure-dokku.sh on your Dokku machine to set Nginx settings to maximum security. On a fresh Dokku install the SSL Labs test will go from "C-" to "A".
Typical command to grab the script and run it on the Dokku machine
wget -O - https://raw.githubusercontent.com/bahmutov/secure-dokku/master/secure-dokku.sh | bash
For more details, read Running multiple applications in Dokku. Another good resource is My First 5 Minutes On A Server and Server configs for Nginx repo.
Author: Gleb Bahmutov <gleb.bahmutov@gmail.com> © 2016
License: MIT - do anything with the code, but don't blame me if it does not work.
Support: if you find any problems with this module, email / tweet / open issue on Github