Let's say I have a PDF called sensitive.pdf with information I don't want anyone to see. I can protect it with a password by running the following command via the terminal:
#pdftk sensitive.pdf output protected.pdf user_pw SuperS3cr3tPW2014If you aren't following the command above you input the original PDF (sensitive.pdf) and output a new PDF called protected.pdf and assign it the password SuperS3cr3tPW2014.
Now you can delete the original file and you can keep the new password protected PDF!
Do you do something else to password protect PDF's in Ubuntu? If so, what do you use? Let us know in the comments!