I assume, that actions like turning/twisting do not work well on touch screens. you can do sliders but for somethings that may not give the correct control. I can probably turn a knob at finer increments than I can slide my finger on the screen.
It is all about haptic feedback, and low latency between action and outcome.
You can twist virtually with good precision. But, what is much harder is the feel, state of the knob, particularly when it is released and then gripped again.
Mechanically, the structure of the knob can take some energy input, and it serves as a mechanical pivot, or fulcrum, depending on how people use a knob.
Without all those physical things, people lack the complex frames of reference needed for fine, "thought is action" type control.
In addition, the essential ship controls must work in rough weather, so you want something you can grasp to keep your hand steady. So long as airplanes have human pilots, I do not suppose the physical stick, rudder pedals and throttles are going away.
The iPod wheel has a physical barrier acting as an affordance for your finger to trace. It certainly works better than it would just floating in space in the middle of a touch screen.
I wonder if it's much easier to process the signal (at the level of measuring and interpreting the capacitances) if you assume a one-dimensional user input. I'm not sure what signal processing happens when sliding on a touchscreen/trackpad.
I imagine the star trek interact can really apply arbitrary forces. So you can simulate a knob for example. Not just a tactile sensation when you're already in (near) contact with the interface.
A really advanced Star Trek interface would use holo/replicator tech to materialize physical knobs, switches, and sliders in a user-defined configuration as they activated the console.
That sort of technology, if scale was not an issue, could allow you to make a miniaturized version of the situation and use your hands to move the ship among the other elements, and that input would then be translated into engine/thruster settings. The model ship would resist movement as needed.
There was no nobs the in their UI as far as I can remember :)
A bigger thing (for me) is being able to sense gaps/shapes without pressing anything and a fixed layout - touchscreens are about the change but that's only good for UI that you look at.