I believe it is rational these days to be concerned with whom you are sharing an Airplane ride with. It is unfortunate that this situation exists but as long as the Terrorists are killing what I perceive as innocent citizens I suspect this added attention will continue and it should.
I would add that the situation might be mitigated some if any Muslim religious leaders or rulers of Muslim dominated countries would publicly speak out against the slaughter of innocents by Islamic radicals. But as long as leaders of some countries are publicly stating "Death to Israel" and "Death to America" and while other leaders in the area remains silent, I think caution is rational.
For the record here I mean no disrespect to any one or to their religion and I believe most Muslims are not going to harm anyone. But as we have learned a few times now in our modern history, it doesn't take very large numbers to do a lot of harm.