How safe are the ferries in Indonesia?

I'm planning a holiday to Indonesia and want to visit multiple islands. I had thought to take ferries between the different islands. However, a lot of people have told me bad things about the ferries in Indonesia, including:

(a) The ferries have far too many people packed onto them, well above the limit imposed for health & safety reasons

(b) The ferries are not seaworthy and therefore likely to be involved in a tragic accident

(c) The ferries will give you a rough crossing to the point of making you ill

Basically, I just want to know if the situation is really this bad. For example, are there safety records of Indonesian ferries to give an objective view of the situation?

To be more objective, some pointer questions are:

1. Are these things really true, or just people complaining without good reason?
2. What kind of things can go wrong if the ferry operators put more people on than the limit?
3. How frequently do accidents really happen on ferry routes compared to how many ferry crossings there are in a year? For example, is it significantly more likely to be killed in an Indonesian shipping accident than in a plane accident?
4. What are the other ways of travelling between Indonesian islands and the benefits/disadvantages of each? Flying is an obvious one, but is this really practical (in order to reach typical tourist destinations quickly enough to fit into, say, a 10-day long holiday) and does it have any similar safety risks associated with local carriers?