I have a website which is hosted on Linux server(Using WHM and Cpanel3) .When I connect it from command prompt with ftp command then everything is ok. But when I try to open it as ftp://domainname.com on internet explorer browser then when I log in not a single file or folder shown me even public_html folder also.
Please try to give me the prpoer reason behind this and also solution if possible.I want to say thanks in advance for your help.

Make sure the permissions of the files are not root, then a regular user won't be able to see it. I'm sure you know how to change permissions.