An application level passcode lock would provide a nice level of privacy and prevent access by unauthorized users on the Scrivener computer. See iPad application Textilus for an example of how such a lock could be implemented. DropBox also provides this feature, but it is less than useful from the PC platform.
iPad programs are substantially different than standard computer software in that by default nothing can even open the files that you create with them, from other programs or even from the iOS device itself. There is no file browser, so no file access, and thus putting a simple lock on the application is enough to block most everything. On the computer however, if you go to a Scrivener project on your hard drive (using the PC will be easiest), you’ll see that all of the files are wide open, using RTF and TXT for the most part. So even if the software had a lock on it, it wouldn’t actually protect anything at all. Anyone can still go into the project folder and read the contents of the project. This can be done on a Mac as well, but you have to right-click on the project and choose to examine the package contents. Then you get a folder view like on the PC.
As AmberV said, putting a lock on the Scrivener program wouldn’t really do much more than provide a false level of security; anyone with access to your document files would still be able to access your files by opening the .rtf files in another text files.
If you’re worried about other people accessing your story, then the easiest thing to do is to set up guest accounts and simply not allow others to use your personal computer account. Both Mac and Windows support this. Alternately, keep your files on an secured usb/external and just unplug it when someone else is using your computer, or invest in actual file security software, which will be a lot more secure than something thrown together by a small company whose main focus is text editing software and not encryption.
Creating a password-encrypted sub-division on your harddrive could also work.
Have you tried TrueCrypt? You can create an encrypted container within which you can store your project, and it will only open if you type in the correct password. When you do type in the correct password, the program mounts the container as a virtual hard drive on your computer, and you can then simply open the project folder the way you normally would.
The program is quite secure, with randomizing hash tags and huge password-length allowances. I’ve read that even FBI computer technicians were unable to crack a well-passworded TrueCrypt container, so that seems very secure. The code for it is open-source, as well, so you could look at it yourself if you were worried something within the code would grant other users backdoor access to your data.
Additionally, you can use TrueCrypt to create hidden containers, or containers within containers, or a container with two different passwords, each one opening a different portion of the container, if you’re that kind of paranoid about your writing.
I’m not sure if it’s available for Mac, but it’s a great Windows freeware program.
For the Mac, the OS has a simple and effective facility for creating encrypted vaults. Using Disk Utility, you can create a new encrypted disk image, which will show up like a drive you’ve plugged in, once you double-click on the file and key in the password. I recommend sparse bundle for the “Image Format” type, as this will expand as necessary as your project grows.
There are also programs that provide a streamlined interface for this. Just be aware that they are repackaging something that comes free with the operating system.
I’d also read through the security advice in appendix D.3 of the user manual. There are a few places Scrivener automatically writes data out, and could expose the unencrypted contents of your work if you aren’t aware of them. Automatic backups is the most obvious, of course.