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As the principal in a web-hosting business, I would respond that generally, you don't give access to "root" to main accounts.
What a hosting company should give you is access to "root" for YOUR account. For instance, if your account is "myname" and your account root is "/home/myname" (a very standard config on linux machines), then you should have access to everything within that directory. Within that account "root" directory is usually a "public_html" folder which is the root of your html files. This allows an area for the web-server to access files, but it can't get 1 level higher -- to your account root. Then, you make a folder in your account root (maybe xoops_trusted) for your protector files. The web-server can't access them, but your application files can.
/home/myaccount - "root"
/home/myaccount/public_html - web "root"
/home/myaccount/xoops_trusted - trusted "root"
Finally, while our accounts can't actually access the /home directory to list contents and/or access files, they can see actual root (linux command "ls /") because some of those files must be accessible and readable for your apps and command line commands to be able to work.
To go to your account "root" folder from a linux command line, just type the command "cd". To find out where you are, type the command "pwd" (present working directory).
Is that clear as mud?