Why don't you use the so-called chemicals that do not damage the rubber. Maybe it will get rid of the sound at the same time. I heard people in here mention some 303 stuff or get those back to black rubber restorer. Won't not using protector make these suckers dry up faster and life expectancy lower. hence rubber damage not likely.
Alot of rubber to protect on the Rogue I notice. Around windows, inside door. So far I just use Armour all thats lying around for the moldings on the bottom/between the windows and around side mirrors but have not touch inside the doors.
Akways thought about the sunroof gasket but been to lazy to do that yet.
I hardly used my nissan maxima sunroof which is why it probably lasted 16 years. Even though I use my my Rogue sunroof more often, others having problems with their sunroof just reminds me that I should not use it as often. I always get paranoid that using something like a sunroof too much would make it break faster.
A guy in a civic forum had the same problem. Check it out:
http://www.8thcivic.com/forums/exterior ... bumps.html