I just bought a PDF, legally, from a publisher’s website. However, in their wisdom, they decided it would be a good idea to password protect all legally-purchased PDFs. This means that each time you open the PDF using Acrobat Reader, you have to remember and type in the password to read it. (Evince, the built-in PDF viewer in Linux, allows you to permanently save the password, but I tend to use Acrobat as it copes better with some PDFs.)
So, if you know the password for a PDF and want to remove it, you can use the command line tools pdftops and ps2pdf to free your PDF from its chains.
Install pdftops. On Ubuntu, you can do:
apt-get install xpdf-utils
Install ps2pdf. I think this is already included with a default Ubuntu.
Convert the PDF to a postscript file, using the password:
pdftops -upw <password> <file>.pdf
Convert the resulting postscript (which is now sans password) back to a PDF:
ps2pdf <file>.ps
The only thing you lose are any PDF-specific features which don’t translate to postscript, e.g. hyperlinks.
Remember, this only works if you know the password for the PDF: it doesn’t break the PDF password for you.