Public buses outside of Jakarta

Most smaller cities rely on mini vans or angkots to ferry you around. There are set routes determined by numbers on the vehicles but they will stop anywhere and everywhere and wait for more people to get in them. The price is cheap though. Bandung is swamped with mini vans. I am not sure about Surabaya.
The public transport in nearly all of Indonesian cities is not comfortable, safe, or healthy but they are all cheap. Motorbike taxis or bicycle taxis (becaks) can also be found.
Most city buses stop running around 10pm and start around 4am.
Better to buy a bike and travel that way.

Wikitravel the cities you are interested in as the site provides some useful information and tips.

I hope some of this helps

Buses range from the luxury coach to stuff that a scrap merchant would reject.
I can only comment on Bandung because that's the only place on the list I've actually been to.
However I assume the other places are the same as Bandung is like every other town's buses.

Local, short range routes tend to be micro buses.
Usually rust buckets and I've yet to encounter a good driver.
If there are laws regarding the number of passengers and overloading, no one knows or cares.
Town to town tend to be a little bigger, a little rustier and the drivers a little worse.

There are no timetables for most buses but they start running when there's demand. That usually means about 5 am.

Thanks guys for the info.  So it sounds like there wouldn't be a lot of problem getting around.  And so what are the requirements for obtaining a driver's license for a motorbike?  Can foreigners do it without being a resident?  How safe/dangerous would you say it is to drive there?  How much would a cheap, used motorbike run?

A motorcycle licence (SIM C) is available from your local police traffic people at a cost of (needs checking) Rp100,000 + bribe.
The licence, if you follow the law, is valid until your residency permit expires.
A 30 tourist visa should allow you a 30 day licence and so on.

A step through moped, in reasonable condition, is likely to cost from Rp6 million upwards.
New price is around Rp13 million for most such machines.

Safe?  I may laugh a lot.

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