I think it's because they're counting on that time being continuous, "rigorous" exercise with an elevated heart rate. I usually average ~14-15mph on my way in but if I'm on a flat stretch my heart rate may not be elevated at all. It's hills and longer rides where the work comes in.

Personally I figure that I'm burning *maybe* an average of 35 calories per mile while commuting but you really need a heart rate monitor to get a better figure. Those sites are mostly ballpark guesses.

I like commuting and it's partially for exercise but the real calories get burned during 30-50 mile road or 18-20 mile mountain bike rides.