When viewing a password-protected PDF from within Safari, or by selecting Open in Preview from Safari's Contextual Menu, the option to save the PDF doesn't exist, nor does the Print to PDF option exist within the Print Dialog box.
However, if you copy the PDF's URL, open the Downloads window (Command-Option-L within Safari) and then paste the URL, the PDF will start to download (i.e. be saved).
[robg adds: A comment on the queue site notes no copy is required; just drag the icon next to the URL into the Downloads window. Note that this hint doesn't defeat the password protection; it merely allows you to download the document.]
Mac OS X Hints