PDDocument doc = PDDocument.load("filename.pdf");

// Define the length of the encryption key.
// Possible values are 40 or 128 (256 will be available in PDFBox 2.0).
int keyLength = 128;

AccessPermission ap = new AccessPermission();

// disable printing, everything else is allowed
ap.setCanPrint(false);

// owner password (to open the file with all permissions) is "12345"
// user password (to open the file but with restricted permissions, is empty here) 
StandardProtectionPolicy spp = new StandardProtectionPolicy("12345", "", ap);
spp.setEncryptionKeyLength(keyLength);
spp.setPermissions(ap);
doc.protect(spp);

doc.save("filename-encrypted.pdf");
doc.close();