There is an overview of that feature here:
To learn how to download a specific flavour for a Kaltura entry ID, see:
Or, to do so programtically, you can use the flavorAsset->geturl() API. An example for that is available here:
This particular example uses the PHP client but the same can be done with any other client you choose to use.
When you say "Will that file be protected?" what sort of protection are you referring to?