Java, fortunately, has a fairly good network of airlines connecting major cities like Jakarta and Bandung, and trains, so going from one part of the island to another isn’t very difficult- though you must remember that Java is pretty big, so travelling takes time. Within Java, you’ll find some very comfortable trains: clean and air-conditioned, but these are usually those which connect to Jakarta- such as the Bima Trains through Yogyakarta and Surakarta, the Parahyangan Services between Jakarta and Bandung and the Mutiara Express, which goes to Surabaya via Semarang. If you have to travel on the less important routes, be prepared for a less comfortable and possibly sweaty ride.  

Besides trains, there’s a good bus network, and you can also find taxis or vehicles for hire- cars, motorcycles, and bicycles; these are, however, usually restricted to transport within a city or town.