The paved road on Ometepe only extends between Altagracia, Moyagalpa, Playa Santo Domingo and Merida. If you're biking or driving, other areas can degenerate fast. The worst roads on the island are probably those on the north side of Volcan Concepcion.
Buses leave Moyogalpa for Altagracia from a station by the docks about every hour between 5:30 a.m. and 7 p.m. From there, some continue on to other destinations via Playa Santo Domingo. A bus to Merida leaves at 2:30 p.m. and 4:30 p.m. There's a bus to Bague at 10:30 a.m. and 3:30 p.m. There's also a bus that goes all the way to the San Ramon waterfalls at 8:30 a.m. and takes about three hours.
This timetable is correct as of July 2008. But schedules can change, and buses are frequently canceled or delayed so don't take it as gospel. Double-check before you risk missing your ferry.