It makes sense, but it means when they went to make Minecraft Pocket for iOS they had to re-write. Must have been a tough decision to force themselves into another re-write when they inevitably want to bring 0x10c to iOS.
Well, Android runs a javaesque language, and still they had to rewrite... because Mobile isn't Desktop.
So not matter what language they choose... they'll have to rewrite for mobile.
That's not right at all. If you write a game in C++/OpenGL you can share >95% code across Win7, OSX, Linux, Android, and iOS. Even if you use DirectX it's not hard to write an OpenGL wrapper.
More impressively if you use C# you can release cross platform using mono.