I think that's a fairly recent introduction. My '04 has no sail-cloth strip in the side windows. Maybe it would help protect the window, but in the 34,000 miles I've put on mine I can't see any damage or harm to windows. If it's scuffed them, it's behind a bar anyway where I can't see it.
It's probably a good idea for it to be there, but I kinda like it without the strip.
2004 Wrangler Unlimited, Shale Green, soft-top, Shrockwork Rocker Guards, Kumho 31x10.5 AT's
Green Jeep Club Member #119