The government isn't investigating the pilot, the airline is investigating. And yes Sunshine, the airline does own the plane.
Thank you for making my point. It is only the government that prohibits religious speech. Not the airline. Nothing the pilot said violated any ACLU/government rule.
When I fly I pray that the pilot is competent, not drunk, and the weather is good. If anyone has a problem with that, I hope they do get off the plane because they may not have my interests in mind!