In ISPconfig, each website is run under its own Linux user and group for security reasons to separate the sites, so that only one site and not all sites are affected in case that a site gets hacked. A ftp user can be assigned only to one Linux system user, so a FTP user can only access one site and not all sites.
You can change the ispconfig sourcecode to run all sites under one user if security does not matter for you e.g. because this server is run in your intranet without connection to the internet. Take a look at the file /usr/local/ispconfig/interface/web/sites/web_domain_edit.php and change the code in the insert and update functions that sets the web user so that the apache user of your system is used for all sites. Ihavent tested it bit it should work most likely.