To be completely honest I commute by bike because I enjoy it. It's more fun than driving, it feels better. Everything else is a side effect or fringe benefit, no matter how beneficial to myself or how altruistic it may seem. If I felt guilty for driving, I'd want to figure out why and fix it.

I went a full year never driving to work, up to a couple of weeks ago. I never felt like I had to ride, and I didn't feel any qualms about driving in after the year. That's how it feels like it should be.