THe meanings which are expressed in English or French with prepositions ('from') can either be expressed by

- a case (Queen of England - Королева Англии. A man of noble )
- or a preposition + a case. (from Russia - из России).

Each preposition needs the noun followed by it to be put in a certain case. Some prepositions are used with two cases (depending on the meaning).

Из always needs Genitive.

The anwser to your question is that there are prepositions after which you must use a specific case. For example, after the preposition "из" you always use the Genitive case.

Take a look at the table here:

http://www.study-languages-online.com/grammar/tables/prepositions-by-case

On the other hand, the words that end in ия have a special declention pattern. Take a look at that too.

из Индонезии. noun+а/и(ы).

Россия - из России

Москва - из Москвы

Берлин - из Берлина

поезд - из поезда

яма - из ямы

сказка - из сказки

книга - из книги

монитор - из монитора

Индонезия - Индонезии

бочка - из бочки

шум - из шума

The same thing with без word. Без Индонезии, без книги etc.

The same thing with из-за word. This word goes before the reason of something. Я плохо спал из-за шума за окном.

*This works with singular only :) Learn this at first, then go to plural))

And remember this:

из-за тебя/него/нее. Я опоздал на встречу из-за тебя!

из этого/этой. Из этой затеи ничего не выйдет!

Don't bother with why's. Just say it. Я из Индонезии - only this way, so we just say so and nothing more.

I believe an ordinary Russian, even educated, when he/she were stopped at the street and asked  will say nothing about the cases. But all of them have strict models engraved on their brains how to speak right.

Just learn models and don't care. And the life will be much easier.