As a matter of fact, even with cushioned shoes, slamming your heel into the ground is bad for you.
If you run barefoot, pay attention to what your feet are doing. Find the lightest, quietest landing you can and listen to your feet. If it hurts, change what you are doing.
The problem with being nearly barefoot is that whatever shoes you have on, no matter how minimal, they shield your feet from the ground. They dull the sensitivity of the feet. (That is what shoes were designed for after all.) Dulling the sensitivity of the feet in any way limits the feedback you get and allows you to continue making mistakes in your running form.
So whatever shoes you are wearing, do your homework, learn about running form, practice safe footfalls, and of course, run like a ninja.