I'm still pretty new to barefoot running, but my experience so far has been that yes, it gets better with practice.  I don't know if my soles are tougher or if my feet are adapting, but it seems to me to be a tiny bit better.

 

Tiny bit better... half a dozen outside runs done.  Lots of short treadmill runs done.

As your feet get stronger and more flexible and you learn to be more relaxed, it becomes much more comfortable.  Your feet will actively conform to the terrain to avoid putting weight on sharp objects.

For now, slow down when you're on rough stuff and try to stay as relaxed as you can.