By Windows users wishing to transmit PDFs securely should consider creating them using PDFCreator. This is an Open Source (and free) application: http://www.pdfforge.org/pdfcreator/download
Ubuntu Linux users may be able to achieve the same using pdftk (PDF ToolKit) which is a command line utility available via the Ubuntu Software Centre. (An application with GUI called PDF Chain purportedly simplifies the process but appears to have bugs and does not work reliably.)
An alternative method is to create the PDF in the usual way, as an exported file from Word for example, and then to use 7zip to create a password protected archive (if necessary with just the single file). All the information you should need is detailed here (the 7zip Help system only seems to document the command line method).
http://www.medicalnerds.com/how-to-encrypt-zip-files-securely-using-7zip/
For Linux systems Krusader seems to do a good job of providing zip/unzip utilities with a user-friendly interface and has a wide range of other useful file management functions including FTP.
Whichever method you choose it is vital that the encrypted file(s) are transmitted to your collaborator separately from the password!