For $50 or less (much less if like me you have an old iPod Nano hanging around), pick up something like a used 3rd gen iPod Nano (i.e., the iPod "fatty"). In other words, one that will charge through your existing iPod cable. Hook it up to your existing iPod adapter and stick it in your glove box as your music player. Leave your phone where it is. Clean, simple, and no more holes.
I realize that if you really need to always have your phone plugged in and charging in the car, this won't do it, although it would be fine if you only need to have the ability to charge your phone when you needed to. Since I usually charge my phone at home, I rarely need to charge it in the car (especially if it is not being used to stream music).