pdfMachine supports PDF encryption, as defined in the "Adobe Portable Document Format Version 1.4".

You can apply security to a PDF either through :

pdfMachine options
You set security enabled in the pdfMachine options if you want the same passwords and security applied to all of the PDFs you will create. Consider using multiple print profiles to set up a dedicated pdfMachine printer to secure PDFs.
pdfMachine File->Document Security menu
If you only want security but just for a particular PDF or you want different security/passwords for different PDFs, you should apply it using File->Document Security menu. This way security does not stay enabled for future PDFs, you have to apply it to each PDF

When applying security you select which operations will be available on the PDF without entering a password, eg printing, inserting pages

Protect Document If checked the security features are enabled.
Encryption Key length AES or RSA (with either 40 bit or 128 bit key lengths) compatible encryption is used. NB. Acrobat Reader versions prior to version 5 only support 40 bit encryption. 128 bit encryption is more secure than 40 bit encryption.
Open Password If supplied, then this password must be entered for the document to be opened. Applications like Acrobat Reader will prompt the user to enter this password prior to displaying the document. Longer passwords are more secure than shorter ones - up to a maximum size of 32 characters.
Permission Password If supplied, this password will have to be entered for users to change document Permissions. Permissions can be changed in programs such as Adobe Acrobat.
Permissions These control what access the user has to the document. NB. If no owner password is present then these permissions can be changed by anyone who can open the document (if they have the appropriate software). Beware; there are programs available that can remove these permissions from PDF documents without the need of an owner password.

40 bit encryption:

128 bit encryption: