I totally agree... It feels natural to have the throttle and brake on the right now because we all learned to ride with the throttle and the brake on the right and the clutch and gears on the left. It felt just as uncomfortable on the right when we first learned as it would have on the left, but over time it becomes second nature and now if you tried to work the throttle and brake on the left it would feel extemely uncomfortable, even worse than if you had never ridden before.

Now why motorcycles were designed with the throttle and the brake on the right is a good question, but there may not be a real answer. Maybe whoever built the first motorcycle just flipped a coin, or was right handed and decided throttle and brake were more important than clutch and gears, who knows.

It is like asking, why do we drive on the right side of the road when most of the world drives on the left? Why do we not use the Metric system when the rest of the world does, etc.