Have any of you used the many calorie counter websites that let you choose an activity and have you input weight and duration to finally spit out how many calories you burn.

I have been baffled by these websites. It somehow doesn't add up at all for me.
I ride an hour to work (door-to-door), and an hour back. It's about 11 miles, that puts me at 1000 calories for the day burned. Which is an enormous amount. I know, I am actually going faster, an average of 15 mph, and obviously I am not actually riding the whole 60 minutes (prepping before the ride, locking up the bike, stop signs, lights etc). But even if you change it to approx 45 min and 15 mph, the calories burned stays more or less the same.

I should be super-slim and fit if I were to burn an additional 1000 calories each and every day (which I am definitely not). I am actually gaining a little weight, maybe 5 pounds over the last year. Anybody else made a similar experience?