I don't have a job so I don't have a commute, but when I did...
Pros:
I felt good getting some exercise.
The cool morning air. The smells of people cooking good food in the evening.
The beautiful ocean and mountain views. Seeing birds and the changing seasons.
Less stress than driving.

Cons:
Getting sweaty and stinky.
Having to carry a change of clothes or else having to ride slow enough not to get my work clothes sweaty.
Having it take a long time to get home.