from Advisory Board member and The Barefoot Book author Daniel Howell:

"Jesus probably went barefoot more often than not; he may have gone nearly 100% barefoot.  There’s some ambiguity in the command to his disciples to take no cloak (extra cloak?) and no sandals (extra sandals?). Certainly he said to wipe the dust from their *feet* if a town rejected them. The confession that John was unworthy to “untie his sandals” may have been a popular saying of the day, or he may have meant it literally. Interestingly, the apostle Paul apparently went barefoot after his conversion because he thought it was proper for a Christian minister to do so. And remember, Jesus (God) told both Moses and Joshua to take off their sandals in his presence and the high priest went into the holy of holies barefoot. Clearly, God considers shoes to be defiling in at least some circumstances.  (Also of interest, the earliest paintings of Jesus almost always show him barefoot; sandals appear on his feet in paintings increasingly after the 18^th century)."

If and when Jesus and other Biblical persons wore sandals, they were likely very primal. The people in those times would have still been able to keep their feet flexible and strong even while providing a protective barrier between them and the ground.