IR touchscreens are actually one of the oldest technologies for touchscreens around. They basically take the photointerruptor - you know, shining a beam into a sensor - and extend it to two linear sets, one vertical and one horizontal. It works with any sufficiently large and IR opaque object, including fingers and (not too thin) stylus, but cannot do multitouch as (generally) two touched points show up as four interruptions - with four possible touches sensed.
The protective layers on the screen are not just sometimes there - screens are fragile. But with resistive touchscreens you have multiple layers, mechanically separated, the topmost of which move. With inductive digitizers none of the layers on top of the screen are involved in the sensor.