Does flying make Superman get all sweaty and stinky? You never see him get all sweaty and stinky.
The big drawback to human powered transportation is our exposure to the elements and the byproducts of our own exertion. We get rained on, and we get all sweaty and stinky. People who can ride short distances without serious hills can avoid getting too nasty. And some employers provide some sort of facilities for protected parking, and even shower and locker facilities. Or the rider might work in a place where being sweaty and stinky isn't as much of a liability.
Superman could definitely commute by air. It doesn't seem to tax him much.