Yes, that's your root directory. Generally on control panel hosting you will have a virtual directory like your describe. Make sure the robots.txt is in the root directory. That way the references to the sub-directories will be accurate.
In other words, root directory is your main directory. So if I was to have a site named www.widgets.com, anything uploaded under widgets.com/ will be in your root directory, aka. main directory.
public_html is generally your root directory where you upload your files. This directory is also the root of your website where you need to put your robots.txt file Read about robots.txt in detail at http://www.robotstxt.org/wc/robots.html
And if you use subdirectories like subdirectory.yoursite.com or forum.yoursite.com you need a seperate robots.txt for each subdirectory
