I do step on carpet and I don't have any problems with the routines. I do however have a problem with the rubber from the top of the step getting on my shoes, then on my carpet. My carpet is lighter and it always looks disgusting because of the rubber from the step.
I'm not sure puzzle mats over my carpet would work very well. It is a thick pile and I am afraid the mats would move too much. Also, I am concerned about having to put them down and pick them up everytime I workout.
I do find hi-lo difficult on the carpet. I think the carpet creates a lot of "drag" and makes some of the moves harder. Also, on some of the Cathe's high impact moves, it is hard to get any height, partially because I am a wimp, and partially because of the drag of the carpet.