It depends upon the design of the bag.

I have seen bags that have a long round section to accommodate the lens, some of these have the lens pointing down.

If it is just an open area for the camera, I place the camera on its back at the bottom of the bag (lens pointing upward).
No scientific reason.
It just gives me a good place to store the lens shade (if so equipped).
I remove the lens shade, reverse it, and place it back on the lens.