In one of our Rails application, we needed to generate password protected PDFs. We used
wicked_pdf (an awesome gem that generates PDFs from HTML template) to generate PDFs but it doesn't provide feature to secure it.
While searching for solution to secure PDFs we came across PDFtk (PDF toolkit). It is a cross-platform tool for manipulating PDF documents. It has feature to add password to PDF document using "user password" as well as "master password" (owner password) which is great.