If the PDF file has a "user" password set (i.e. you have
to supply the password to open the file in Adobe Acrobat
Reader), APDFPR can decrypt it (removing the protection)
only if you know either "user" or "owner" password. The
user password itself can be recovered using brute-force
and dictionary attacks only (which are time-consuming);
if you're interested in such features, please look at
"professional" edition of APDFPR:
http://www.elcomsoft.com/apdfpr.html