Of course it does.
None of us have to train to run 100 meters. You go outside and run.
Anyone here can go to a pool and jump in and swim as well.
You have access to either rather easily(for example, you pay taxes and can go us the facilities at a community college).
To be able to swim that distance, you need to train and get your endurance up. To be able to run that distance, you just have to be able to move.
Even the most out of shape person can run/walk 100 meters. I don't think most could jump in a pool and swim the whole time and get there. And when I say swim, i don't mean stop and tread water or float on your back to rest or anything like that. I mean continuous movement towards the wall doing an actual freestyle stroke( we aren't doggie paddling either although I doubt they could do that either).
I really don't get the logic here.
Lets go through your points...
1) Anyone can run. Sure, I agree.... the fact that anyone can, means there is more competition, and Bolt is dramatically faster than anyone ever.
2) Anyone can swim. No, this isn't true. There are lot of people in the world without access to a pool, or water for that matter.
3) To be able to swim that distance, you have to train. For the people that have access to water, and learn to swim... those people don't have to work any harder on their craft (in this example 100M) than a runner has to work on theirs.
4) Even the most out of shape person can run/walk 100 meters. All that speaks to is the idea that more of us spend more time walking / running, than we do swimming. Even if the running is more natural, that doesn't make swimming more difficult.