Here are the options that I see for you. I have attempted to correct the answer that you graciously accepted before I took in account that your folder is on your Wubi /host filesystem and that makes a huge difference.
Option 1. Encrypt your folder using EncFS. You'll need enough working storage somewhere in order to create the encrypted folder. In Windows you could use encfs4win (free, "experimental") or BoxCryptor ($40) to encrypt and decrypt the folder. In Ubuntu you would use EncFS and FUSE as explained here: http://www.arg0.net/encfsintro
Option 2 (incompletely worked out). It sounds like you want to prevent some other Ubuntu users from accessing that folder when it is mounted. For that purpose, another method is to use file and directory permissions rather than encryption.
There's a difficulty here. Wubi doesn't enable you to control the Linux ownership and permissions for the individual Windows files and directories on the partition containing the virtual disk(s) (which it puts in /host). You can control the Linux ownership and permissions for the partition as a whole by editing with
gksudo gedit /etc/default/grub the ntfs-3g "uid", "gid", and "umask" options in line
GRUB_CMDLINE_LINUX_DEFAULT="rootflags=<options go here> quiet splash". If you need more information about the options, that can be found in
Option 3. Move the 100 Gb folder to a separate NTFS partition or drive. Then you could use the normal /etc/fstab mechanism to mount it and the partition-level permissions and ownership would be sufficient for the access control that you need. Again you would need information about the options from
Option 4 (incompletely explained). Converting from Wubi to a real Linux partition would make it possible to mount the Windows partition via the normal /etc/fstab mechanism. Then you could reasonably consider building ntfs-3g from source with the
--enable-posix-acls in the
configure command. That would give you control over permissions in a manner that is compatible between Linux and Windows. Further information: http://b.andre.pagesperso-orange.fr/permissions.html
In any case, make sure that those other users don't have root access. Normally they do not, but you'll want to be sure. To prevent specific Ubuntu users from having root access via sudo, you can "open the Users and Groups tool from System->Administration menu. Then click on the user and then on properties. Choose the User Privileges tab. In the tab, find Administer the system and [un]check that." (Quote from https://help.ubuntu.com/community/RootSudo)