After looking over the counter-arguments you have provided and talked a Muslim friend of mine, I have come to the conclusion that like many other religions, it is possible to "interpret" out of the holy book pretty much whatever you want to interpret.

I think that the way the Qu'ran words it, you could legitimately interpret it the way that that blog post did, and I think that you can legitimately interpret it to be peaceful. (Not that that makes the Qu'ran legitimate. I hate that religious books aren't perfectly unambiguous.)

Based on this I think that we should judge the individual, not the religion.

However, based on statistics, it has been members of this religion that perform terrorist attacks, so profiling makes sense. I just don't think it needs to be done in the manner described in this story, especially for U.S. citizens.

In my ideal society, we wouldn't even have airline security for U.S. citizens, regardless of religion. This means that every once in a while, a terrorist would slip through the cracks. But such is the price of freedom. Perhaps even the good guys on the plane would be armed and take out the bad guy before he could cause harm.