If you never use your docking station, put a piece of tape over the connector

Not if you have the accidental damage coverage. If you have the normal warranty then you would lose the warranty on the affected part (probably the connector / main board) but not, I think, on unrelated problems.

John

 

You'd think they would make some kind of rubber/plastic plug that you could put in it when not being used, one that would be very flush with the bottom of the case.

 

I think that wouldn't work. The docking port gets very hot on some laptops, so hard plastic might work, but rubber would scare me. Additionally one would easily loose that part. You can't just fix it with a hinge or wire on the underside of a laptop.
But the idea itself seems reasonable. I think some slider made of the same material like the bottom case would be good. This would mean that the docking port would have to sit deeper in the case which might be a problem for current docking stations. But one could easily ship an adapter (basically an extension) with new laptops that stays on the docking station.