Discussion on:

Safeguard your data with Wise Folder Hider

did you check with a live distro to see if the hidden / password protected folders were hidden from linux?
I bet they aren't

edit to add:

If I'm right and they aren't hidden or protected, then I would say that encryption is still the only real option. and truecrypt is also free.

Tell you what I'll encrypt my secure data instead. That way it's more secure and better still I'd don't have to turn off the security I have for a UI feature.

Sheesh