To protect your shoulders, you'll just have to be careful. As far as I know, there's not a way to do the exercise right and restrict the stress on the shoulders. You can do the roll-outs from your knees, and you can use a wall in front of you to limit your range of motion, but a full roll-out will definitely put stress on the shoulders, not that there's anything wrong with that.
If your wheel is set up to attach to your feet (will have straps) you can stay in the pushup position and use it that way, though it's a totally different exercise.
For more info on "The Wheel", you might check out the work of Ross Enamait. He has one video where he does full wheel rollouts with multiple weight vests on. I don't know how he survived.