Clans
The main reason for clans — and other subgroups like them you'll find — is to give an idea of what kinds of characters are likely to be found in a typical game, and give you some inspiration for what kind of character you'd like to make. They offer some easy-entry stereotypes, some starting conflicts (Lion are rivals with Crane; Crab think the Scorpion are sneaky and untrustworthy while the Scorpion think the Crab are boorish thugs), and access to mechanics that are exclusive to the clans — a Dragon spellcaster will feel different in play than a Phoenix one.
Artisans and Geisha
They're not "classes" like character classes; they're social classes. You might enjoy playing one, but they're included as alternates to things like shugenja and samurai, which are more typical character types.