Definitely the tach cable. I would say that if your bike doesn't currently have a tach, that it might be a good idea to cover the hole with something so that dirt and other miscellaneous particles don't get in there and gum it up.
Did the bike originally come with the rubber stopper in that hole? If so and you don't notice that it is causing any damage for now, I would leave it. If you have plans to put a tach gauge on the bike then obviously at that point the end of the tach cable would go there and a screw is then inserted through the side to hold the cable in place.
I am kind of new on this forum so if that doesn't sound right to anyone else who is more experienced please throw your two cents in!
Good Luck.
Judd