If you would be able to access all sites from one FTP account, then a hacker that gets access to one of your sited e.g. when there is a vulnerability in one of the installed cms systems would be able to access all sites as well. This makes cpanel quite insecure. ISPConfig isolates each site by assigning a different Linux System user and group to the site and all php scripts run under this Linux system user and group. As a FTP user can only be assigned to one Linux System user, you can access only one site with a FTP user.
In ISPConfig 3.0.5 beta 1 there has been introduced a new feature that allows to add domains inside a existing site similar to what cpanel offers, but personally I wont use that on a server which runs websites that are connected to the internet due to the fact that a hack into one of these sites will affect all other sub sites as well.