To a large extent, OS X gives the best of both worlds.
From the command line, things look very much like you describe (but not exactly, Apple often has different conventions and names for things than Linux, say). That application you just downloaded is just a directory with a ".app" extension. You can browse its directory structure and find all of the resources for the application, all residing in their conventional locations.
But using the Finder, you just see the application's icon. If you double click it, it launches.
This is just one of the ways that Apple manages to have Unix underneath, but not expose it to users who don't want to care that it's there.
From the command line, things look very much like you describe (but not exactly, Apple often has different conventions and names for things than Linux, say). That application you just downloaded is just a directory with a ".app" extension. You can browse its directory structure and find all of the resources for the application, all residing in their conventional locations.
But using the Finder, you just see the application's icon. If you double click it, it launches.
This is just one of the ways that Apple manages to have Unix underneath, but not expose it to users who don't want to care that it's there.