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Flip the Seat Belt Fastened sign on...then they will have to stay in their seats.
I would say no...
I don't think passengers have as many "rights" as many people would think. While on board a Delta (pick an airline) flight, passengers are in a place of business that has policies just like a department store or restaurant.
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I am not saying that any passengers have a "right" to pray. I just don't see why if they are respectful and peaceful it would be a problem. As a courtesy, would it not be the right thing to do to let someone pray if they wanted to pray? If other passengers began harassing the muslims just because they were praying, then it would be the passengers that were in the wrong, not the muslims. (And those disruptive passengers would be in violation of the FARs, and on my plane, I would let them know that.)
I would personally not be uncomfortable to see someone praying on a flight, and if I did become uncomfortable, it would be cause for me to look at my own prejudices, not blame them for being who they are. (Keep in mind, being an atheist, I get uncomfortable when anyone prays...lol)
That's my opinion anyway.