If you wear just socks indoors as much as possible, that should help the soles of your feet toughen up over time.
The shape of your feet could be another factor, especially if you are quite flat-footed.
I've always felt comfortable going barefoot, but I have high arches and short wide duck-shaped feet, pretty much as per the 'primal' shape. The downside is that it's difficult finding comfy shoes that I like.
F 5 ft 3. HW: 196 lbs. Primal SW (May 2011): 182 lbs (42% BF)... W June '12: 160 lbs (29% BF) (UK size 12, US size 8). GW: ~24% BF - have ditched the scales til I fit into a pair of UK size 10 bootcut jeans. Currently aligning towards 'The Perfect Health Diet' having swapped some fat for potatoes.