I don't normally go out of my way to watch flash video but I had never noticed the fan while playing any video but your post caused me to wonder a bit. I went to flashcomguru.com:
http://www.flashcomguru.com/apps/fullscreen_player9/fullscreen.html
and played the video full screen over and over on my 2011 i7, starting the next playthrough immediately after the previous one finished. I know very little about the various editions/makeup of flash videos so perhaps the ones you watch provide a much greater load to the CPU/GPU combination. You might try that to see how your temperature rise compares to mine using the same flash video.
The temperature of my CPU started out at 35deg C. After the first playthrough it had reached 53deg C. After the second playthrough it reached 60deg C. Further playings did not cause the CPU temp to rise above 60deg C and I played about dozen times after reaching 60deg C.
Throughout the testing the fan speed never rose above 2k.
I should also note that I have a Speck clear 'case' which covers both the top and bottom of my MBA so the cooling from convection is likely less than w/o the protective cover.