PP9 or PP10 allow production of PDF files with password protection. There are programs around that will circumvent standard PDF protection, but if basic protection is enough it will do the job very well. Good for formatting the book properly, and for professional printing via high quality PDF. Supports URL links, bookmarks, various compression for a web version, etc.
If your book is already finished, and nicely formatted in another program, you can use a PDF printer driver like PDF Factory Professional, click here - which is cheaper than the full Adobe Acrobat