I don't use the stem nuts, as they don't work very well on aero profile rims, and I prefer smooth valve stems for reasons already mentioned. I like keeping the valve covers though. At least until you lose them, they do give some protection, and since I have a Lezyne pump on one of my bikes, having a clean, undamaged presta thread is important to get the chuck on and off. Also, when the tube is rolled up, the cover prevents the stem from stabbing things inside your seat bag or jersey pocket, not limited to the tube itself, or the baggie the tube is in (if you like to talc your tubes).