And what is to stop someone from saving the content displayed in the webpage and sharing that just as they would with a PDF? Heck, the user can just "print" the web page to a file (PDF, HTML, etc.). Anything that is viewed on a webpage can be copied (even if you try to implement some javascript hacks - which you should NOT do). Storing the content in a database does nothing to prevent this type of tampering either.
Regardless of whatever method used to deliver your content (PDF or HTML) - it doesn't matter. I think your concern is about people directly accessing the content. That is easy to control - don't put the files in publicly accessible areas! Put them in a directory that is outside of the public folders. Your PHP files when being processed will be able to access the files, but a user could not access them through a URL. After you validate that the user can view a particular resource) just include the file in the output. That will prevent unauthorized access to the content from your web server. But, as stated previously, once you present content to a user, there is really nothing you can do to prevent them from copying/saving the content.