The bus station is 1.5km outside town; taxis cost around R$20 to the ferry or the center.
Rota (www.rotatransportes.com.br) buses go to Ilhéus (R$63 to R$75, six hours, four daily). Rota also has one daily bus to Itacaré (R$87, eight hours). You'll have more options for the same trip if you're willing to switch buses in Ilheús. Águia Branca offers one daily departure to Salvador (R$146, 11 hours) – an overnight bus at the time of writing. Águia Branca also runs the long haul to Rio de Janeiro (R$306, 22 hours, including a connection in Vitória.)
For more frequent connections, three companies run buses to Eunápolis (R$15, one hour, every 30 minutes from 5:30am to 10pm).
The balsa, a quick car and passenger ferry, connects Porto Seguro to Arraial d'Ajuda (R$4.50, 10 to 15 minutes). From Arraial's port, you can catch buses into town, or to points further south like Trancoso.