There's a huge difference between Jews and Muslims praying on an airplane.
When a Jew prays, the worst that can happen, is he might be in your way, and will mysteriously not acknowledge you when you say "excuse me" (a portion of Jewish prayer - the amidah - requires the Jew to stand in one place with his feet together, and be deeply focused on the prayer).
On the other hand, when you hear someone on a plane say "Allah huwakbar," you'd best start praying yourself.
So what's the big deal? The Muslims are upset, because they were treated like we're at war with them. Well, guess what?
WE ARE!!!