Most of mine have been covered already, but I'll chime in.

Pros:
Commuting saves me a gallon of fuel a day.
Keeps me in shape (A friend keeps commenting on my ever shrinking beer belly).
I tend to get depressed, cycling keeps that at bay.
Gives me more reason to collect and wrench (Eg spend $$) on bikes.
If I get up early enough I can ride 80% of my commute alongside the Boise river.


Cons:
Time.
My car drive is 15-20 minutes, the bike ride is 45min-1 hour.
Cost.
Despite most things being a "buy once" type item, new bike parts and clothes for changing weather can be substantial.
Weather.
I don't mind snow, rain or sunshine, but a headwind is the bane of my existence after a long day.
Social pressures:
"So we're all hanging out tomorrow after work, you should drive so you can join us".