It was the exact opposite of his boat service in Wind Waker. That one made sense since everyone had to travel by boat or lived on an island. But Skyward Sword Beedle? Dude didn't want business, I guess! I suppose you could make the argument that people could use the birds to get to his shop, but that's an awfully small needle to thread without Link's equipment.
In other news, I have thought about this too much, and I have been up for too long.