How to test native Android app with Protractor
As you pointed, you want to test an Android native application. You would need to use other framework for testing native apps.
On the other way, Protractor "is an end-to-end test framework for AngularJS applications". http://angular.github.io/protractor/#/
So, it runs on a browser. The browser could be on your PC with WebDriver on your phone with AndroidDriver. But never a native application.