You might be confused about the specific differences between apps, so I've put together these definitions to help clarify.
Native App - Native apps are apps built directly in the device's specific language. For instance, iPhone's is Objective-C, Android is Java, Windows Phone is C#.
Hybrid App - A web app that has the look and feel of a native app but is still built with HTML/CSS/JS.
Compiled App - A compiled app is a web or hybrid app that you've ran through PhoneGap's Build service to create "native" apps.
I made up the last one, but I felt there needed to be some sort of way to differentiate non-native apps from native apps that were built by running a JS app through a service.