No. You should never be uncomfortable during a massage. If you feel discomfort during a massage (ashiatsu or not), speak up. A massage professional needs, and wants, to know.

People who desire deep tissue massage often report less pain from ashiatsu. This is attributed to the increased (broad) surface area of the foot. Pressure from the foot or heel is distributed over a larger area, therefore the pain is less intense than pressure applied from the thumb or elbow.