I'm pretty sure that Muslims are required to pray five times a day, at set hours. That's why the "prayer call" sounds in places like Dearborn.
I believe the Koran is very lenient on this requirement for people who are traveling.
I know it is very lenient toward travelers during Ramadan, allowing those on journeys to eat and drink during the day.
There is no absolute requirement that you HAVE to do your prayers at set times if it is not convienient.
And anyway, the perception of the other people on the plane that something was wrong is still based on the knowledge that the terrorists did their jihad prayers before taking over the planes on 9/11.