The root is the folder where the website files for a domain name are stored. Because cPanel allows for multiple domain names (addon domains and subdomains), you need to have a unique folder for each domain.
Your primary domain is rooted in the public_html folder. Your addon and subdomain names can be rooted to their own folders inside the root folder, or in their own folder in public_html. After you create an addon domain or subdomain, you can find the document root inside cPanel by clicking on the Addon Domains or the Subdomains icon.