A small flap that moved aside when inserting a cable would solve the problem with dust in the port. I am actually surprised the dock connector doesn't have this.
I remember when they first introduced the dock connector with the 3rd Gen iPod and the iPods came with an insert for the dock connector when you weren't using it.
Until dirt gets up in there and prevents it from opening. The only real way to do it would be to cover from the outside, and that would stink. Maybe a plug you can put in there; a DockPlug.
I had a Samsung phone that had one for the power port. Broke about two months after I bought it, never cared. Buy a paperclip every 3 months, it's not that hard and looks much better.