If I assign more then one website to one use, why would I want more than one system user?
Thats a question of security. If one client has lets say 20 websites and all websites have the same user, then he will loose 20 sites if one of the sites get hacked e.g. trough a insecure forum or cms system. If every site has its own system user, only one site will be affected.
The drawback is that the user will have to use a separate FTP login for every site, but this can be circumvented if the user says that he wants to access all sites with one user, he can make the files group writable for the client group.