Since biblical times, this life-cycle ceremony has held much symbolism for Jewish people. Your son will probably look different from his father in many ways. He may have green eyes, while his father's may be brown or blue. He may have wavy light hair, while his father's may be dark and straight. His will have soft, smooth skin while his dad may have hair on his arms and back and need to shave every day.
Children realize that they look different from their parents in all sorts of ways.
Your son will learn that his mommy's and his sister's anatomy is quite different from his own and his dad's. Most likely he'll accept these differences between females and males readily and comfortably. Children also accept that their hands, feet and other body parts are naturally smaller than their parents' body parts. By the time your son is able to ask questions about foreskin differences, he'll probably be old enough to understand your answers. In my work with interfaith couples, I have found that it is more often the uncircumcised dads who have feelings about their circumcised sons looking different from them.