There's a lot more to an application than its configuration. It may require certain specific system libraries, need a certain way of starting up, or a whole host of other special things. With a container, the app dev can precreate a perfect environment for their program and save you LOADS of hassle trying to set it up.
The benefit of all this is that you can know exactly where application state is stored, know that you're running the app in it's right environment, and it becomes turbo easy to install updates, or roll back if needed.
Totally spin up a VM, install docker on it, and deploy 2-3 web apps. You'll notice that you use the same way of configuring them, starting and stopping them, and you might not want to look back ;)