Is it a long bus ride? Some kids spend a lot of time on the bus, making stop after stop after stop to let other kids off. For others, it's a brief time on the bus. Evaluate the length of your son's ride.
Is he tired? Does the thought of walking up those seemingly tall bus steps just too much for his little legs at the end of the school day? How does he act when he gets home? Does he fall asleep for a nap, like the day was just too much?
Does one of his little friends get picked up?
Is the bus pretty much just for kindergartners, or are there also much older kids on the bus who may be pretty rowdy (that can be scary for a little kid, even if nothing wrong is happening - it's just noisy and exuberant).
Look at the big picture. If it's a reasonable length of time on the bus, a safe bus with a pleasant or at least polite driver, if there are not a lot of older kids on the bus, if he doesn't get off the bus crying or roughed up, then just tell him that school kids ride the bus. Greet him with a healthy snack and a hug and he'll be ok.
Some kids just have a sense of how they think things should be, or they take one small incident and their little brains just think "that's the way it's always going to be" when it was just once that a kid got sick on the bus, or just once that the bus passed a traffic accident and the kids saw the ambulance. Or little Joe says his mom always picks him up, and how he doesn't have to wait in the bus line, but your child may not realize that Joe's mom picks him up because they live 20 miles away, or Joe goes to violin practice every day after school.