If any security features are turned on by the creator of a PDF document, the PDF file will be encrypted. These security features let an author disallow printing, copying text/graphics, editing, and/or adding annotations.
The Xpdf package honors these permission settings. Specifically:
I occasionally get email asking if I can explain how to crack a PDF file, or if I can help decrypt a PDF file. I won't help these people because I believe that an author's requests relating to the use of his/her work should be honored.
I distribute source code (for Xpdf) under a particular license (the GPL) which depends entirely on users' goodwill for its effectiveness. If any of my users ever decided to violate the license, I would probably never even know about it, much less be able to do anything about it. The only thing I can do is trust the users.
In light of this, it would be very hypocritical of me to, on one hand, ask people to honor my licensing restrictions, and, on the other hand, bypass (or assist others in bypassing) another author's requested restrictions.
In addition to all of this, Adobe requires that implementors of the PDF spec adhere to the document permissions.
"But copyright law allows me to quote parts of a document under the fair use provisions -- and Xpdf is preventing me from doing that." Not really: you're still free to quote the document the same way you would a newspaper article, i.e., by retyping the text. If I have to choose between honoring the author's request and trying to interpret the law (exactly how much does fair use allow you to extract? should Xpdf allow copying a certain amount of text out of protected documents?), I'll choose to honor the author's request, no matter how misguided. For those who would argue that important content might get irretrievably locked away in PDF format, I'll remind you that Xpdf is open source, and can be modified by end users (the GPL even allows this).
If you think these security protections are a bad idea then write the author of the document. He's the one who set those bits after all.