I've come to believe (perhaps incorrectly) that running barefoot requires more of your calves and less of your thighs than running with conventional footwear. Do you perform any exercises specific to your legs, and perhaps your calves, besides running?
I’m still learning but you definitely work out muscles in your calves, shins and ankles more when running barefoot. That and a bunch of muscles in your feet (i.e. arches). I’m not sure if you use your quads less. Right now I’m not doing any special exercises other than running drills once or twice a week (high knees, butt kickers, high skips, karaokes).
For me, I think just slowly increasing my barefoot mileage and giving proper recovery time in between runs will strengthen those “new” muscles. I think some of those muscle were already pretty strong from the amount of running I was doing (just finished a marathon in February) and the cross training (cycling, mountain biking and swimming).