Fantastico lets you install scripts directly from the control panel, handling everything for you (creating the directory, creating the database and db user, copying files to your server, etc.), which is easier for less-experienced users, but there are a few disadvantages:
You may not always get the latest version of a script - it takes time for the update to get to Fantastico, and it may be even longer if your host has Fantastico configured to automatically update itself.
You may not get the same control when installing it through Fantastico as you would when installing it yourself. For example, with SMF, Fantastico will install all 30+ languages, which requires several additional MB of disk space. The user does not get to choose which languages to install.