Yeah, so anytime some Muslims pray, they've got to be carrying bombs on them and they're ready to blow themselves up, right?
Having said that, a little consideration on the part of everyone goes a long way. If you know there are a bunch of ignorant Aunt Bessies who think that if you're saying prayers to Allah you're going to blow up the plane, it'd be a good idea to pray silently.
And if you're the crew of the airplane, you could tell Aunt Bessie that they're simply praying and there's nothing to worry about. If she insists on equating praying with terrorism, well, put her on the next flight and hope that no Shintos start praying.
And if you're Aunt Bessie, you might want to get your head out of your butt and say to yourself, hmm, if I were a terrorist looking to blow up the plane, would I want to draw attention to myself?