Perhaps the reason for the relatively low visitors is because of the recent problems in Bali. The Bali bombings of October 2002 has given Indonesia a fairly negative world wide impression of the safety of the country. The recent blanket warnings against travel to the archipelago by the foreign offices of the US, the UK and Australia have reinforced this perspective and severely hit the tourist industry.
It cannot be denied that Indonesia has had a troubled past, but fortunately it seems to have emerged from these times and moved on to a happier future. Travel round the country is safe and easy in the main tourist areas of Java, Bali and Lombok. Further afield than these areas, travel can be more infrequent and slower but is still by no means dangerous. Violent crime is a rarity although (as with anywhere) obviously not unheard of. Crime that you do need to be aware of as a tourist will take the form of con tricks. There are a few well known tricks, most notably the batik scams in Yogyakarta, but if you use your common sense when conducting transactions then you should avoid trouble. Political troubles in the archipelago are not unknown, so its best to keep up to date with travel warnings and ask around locally before you travel to areas you suspect may be volatile. If you stick on the main route of Java-Bali-Lombok however, you should not encounter any problems.
Travel round the country can be a little trying at times. Despite the abundance of methods to get around the country, travel often requires a certain amount of patience. The relaxed pace of life is reflected in the transport systems, with the local transport often waiting until full before departing and crippling traffic jams in cities producing further delays. Consequently you should allow more time for travel than initially expected. It is very rare for transport to actually arrive at your destination at the time you are told, and this can mean that you may need to spend nights in commuter towns you were not expecting to. Trains prove to be more reliable than transport by road although they have limited scope for travel as lines only run through the north and south of Java. Boats are often quite efficient although these are still affected by weather conditions so are still slightly unreliable.
However there are two advantages to travel in Indonesia. Firstly is it is very cheap. On local buses, an hour long journey will cost around 7,000 Rupiah, and bemo's and colts can be cheaper still. Long distance overnight buses cost significantly more (aprox. 100,000 Rp for a 12 hour journey), but these tend to be pretty luxurious. The other main advantage of travel is the scenery. Once you are out of the cities, the scenery on journeys is often incredible. It is incredibly easy to wile away the hours on long journeys by gazing out at the fertile volcanic landscape passing by you.