Located out of town to the east, Ruteng airport has flights with TransNusa to Kupang three times a week.
Transports to most major destinations in Flores can be arranged through your hotel, though try to book early as they do fill up.
Sample fares include Labuan Bajo 80,000 rupiah, Bajawa 80,000, Ende 180,000 and Maumere 260,000.
If your hotel can't help you, head down to where the drivers all hang out near the Sindha Hotel and ask there for a seat. Early morning is the best time to try.
Rima Hotel can arrange car hire at 800,000 rupiah per day (including driver) and motorbike hire for 100,000 rupiah per day.