I had a lot of difficulties re-wiring my expectations with this as well. jQuery ‘queries’ the DOM and manipulates it - but with no care for any application ‘state.’ When you refresh an HTML page - the whole thing is read again / js / CSS / HTML. With Ember, you are creating new DOM or 'view’s or whatever - depending on the template and route or component. For these portions of the UI to be aware of their state, you work with the Ember object to access the benefits Ember offers you. Where I do find myself using jQuery, is when I create a component to initialize a plugin like ‘flickity’ - (and then to destroy it when the component is no longer being used)
It’s definitely something that could be better introduced since not everyone is coming from a predecessor framework. It’s the kind of thing where people say “you’re doing it wrong,” which isn’t very helpful - and kinda sounds rude - but is the answer. I still struggle with it myself.