When you upload a site to a Linux/CPanel server, you need to make sure that the content goes where the server expects to find it. Your folder on the server's hard drive contains a number of sub-folders (like mail, public_ftp, public_html, and so on) and the correct content needs to be in the correct place.
So, when you upload via FTP, you need to make sure that your FTP client changes into the 'public_html' folder first, and then upload your content into there.
