subdomain and addon domain

i have heard that ranking a sub-domain is hard and some time even if it ranked google finds that if it is sub domain then it get dropped , my question here is my webhost provider allow me to add 5 website to my account and i add this from cpanel as addon domain will that be consider as sub-domain in google's eye , when i check the ftp the site are listed like this the main site in the public_htm then rest of the site is in the folder named site1 ,site 2
if i add a sub-domain also the file structure is similar . please help me with this