You will still need to use @media if you want your interface to work well with different screen sizes/orientations.
JQM does a great job for most things but for example if you have a tablet landscape then you don't want a horizontally stretched long scrolling pages where you could have a nice side navigation, where on a portrait phone screen there is simply no room.
I use the @media mostly for controlling the navigation elements that appear and dissapear depending on the screen size and orientation...it's actually a pretty simple once you have a couple of css classes defined you simply attach them do the JQM buttons or divs and you end up with a more ergonomical interface.
For example I was anoyed that a form was stretching too much on a landscape tablet screen so I now have a class that changes the form width depending on the screen width, so for a tablet it's nicely centered with space around but for a phone screen it's stretches to cover most of the screen.