If it bothers you pull it out,
Personally, I like having it in, it's piece of mind on long trips. I had a BMW before that didn't have a spare, and I really wish it did on long road trips.
Plus, I actually hate the ride of run flat tires, so I'm glad the spare is there because I will be getting rid of the run flat tires for a lighter, better handling, and riding tire.
all that being said, I may take my spare out and only put it in my jeep when I plan to do longer trips where I may be crossing areas where I won't be seeing a service station for miles.