If you were literally barefoot, would you come down heavily on the heel below the ankle?
No, your natural instinct would be to rotate the ball of your foot downward to create a mid-foot strike.
THAT is the problem. I had the same issue from years of "running/basketball" shoes.
Once I started wearing Vans, I re-adjusted the stride, and then transitioned cleanly to Vibrams.
If it HURTS, your mechanics need tweaked.