There are 2 bus systems that will take you into town for $5 dollars round trip. The return ticket is only good with the bus company you went in to town with. On Sundays there is a small sightseeing train that runs into and out of town. Tours to the reef or rain forest pick you up at your hotel.
Buses go past 4 times per hour from 7AM til around midnight.
The main downtown area along Macrossan St is easily walkable if you choose a hotel/hostel in that area.