I noticed in many examples, KeyPairGenerator is used to generate public and private key. Every time you run the program it generates different key values.

But in real world, who want to generate the key's again-again. It would be done one time only.

Do organisation's run standalone program to generate the key's and then save in DB to be read by other server programs to encrypt/decrypt files?

It varies, some do, some don't. People use everything from smart cards, hardware adapters, file based key stores, to data bases.

Regards,

David