Because you did it the wrong way.
Generally you don't create your application in public_html folder - kohana is a framework.
You should create a new controller in application/classes/controller/admin/index.php containing (Controller_Admin_Index extends Controller_Template) - there you will have your application. Routing can be set in bootstrap.php
I repeat - you create your application logic in application/ folder not public_html/ folder.
Long way to learn brother
E-mail me email@example.com so maybe I can help if you are willing to do the heavy pushing yourself.