I remember the Prefix once was incented, because a lot of hosters only supported one Database per users, so many applications needed to share one database and it could come to conflicts. Also the prefix enabled you to install more then one magento into the same Database.
But, is there still a reason for them today I do not see?
Even on a free hoster you get by far enough databases what I know.
Best Answer
First, there still may be some people who have a limited number of databases and can use this feature. And there may be people who find it handy to have it all in one database, although I would never recommend it. In my humble opinion, separating the databases is always better.
Second, it may also be a security concern. Having a prefix for your database tables makes it harder for an attacker to guess the names of the tables and do stupid stuff.