I really don't think racism is part of the problem. Im not saying there aren't racists out there, but after 9/11 99.9% of the American flying public get uncomfortable if they are on a flight with "muslims". There's lots of people that don't think they have a racist bone in their body, but when they see a person sitting 2 seats away that could be perceived as a "muslim" their mind starts thinking. Most people won't say anything, but it does happen.
I'm not saying what the captain did was right. Personally, I would have let them fly, but if you want to call him a racist then you also have to call 99.9% of the flying public racists also. If you would have removed the passengers who were a uncomfortable then the two muslims would have been the only one on the flight. Thats just how people think now, and it will take a long time for people think otherwise. Its just like how people are scared to fly in the first place. You can give them all the facts and tell them you're more likely to die on the way to the airport than on the flight itself, but most people still get nervous while the airplane is throttling up for take-off. The facts and statistics are there, but it doesnt change the way they think.
Let's face it... 9/11 effected more than just the twin towers.