Why isn't Bug supereffective against Ground?
This was most likely done for balancing. Ground already has three weaknesses, to Grass, Water and Ice. And well, a single bug isn't going to do much to a giant piece of earth.
Why aren't Flying attacks supereffective against Ground?
Again, probably balancing. If you think about it, a bird can't really hurt a piece of earth. What's it going to do? That's my take on it.
And of course, Gamefreak logic.