Angular supports many styles of markup. Other valid forms of that snippet are:

Using xml namespace: <input type="checkbox" ng:model="todo.done">

Using underscore in the attribute name: <input type="checkbox" ng_model="todo.done">

As an x-* attribute: <input type="checkbox" x-ng-model="todo.done">

As a HTML5 data attribute: <input type="checkbox" data-ng-model="todo.done">

I think their may be a few more, but in any case, Angular is flexible enough that you can choose the representation that is best for you and your team.

You must like bloating your project with pages of trivial javascript accomplishing trivial functionality.

I really don't want basic stuff in my application logic.

Allowing users to flip arbitrary booleans is a bit like declaring a public variable though. You can of course make them go through a setter if you prefer encapsulation.

<input type="checkbox" ng-click="setDone($event.target.checked)">

This was a deal-breaker me, when I was evaluating Angular and Ember ~6 months ago. I eventually chose Ember and things worked out pretty well.

What about it do you find terrible? The declarative nature of the binding? Or just the fact that it isn't valid according to the HTML spec?