I don't see that there'd be any effect at all. The Fly America Act already require that someone travelling for the US government to say, Dubai, would fly on a US carrier instead of Emirates. Of course, no US carriers fly direct to and from Dubai, They'd be required to fly KLM to AMS and then Delta to the US (For example) so this ruling wouldn't affect them.
That's what people are finding suspiciously convenient about this move. Maybe there's good security reasons, maybe there's not. But there's no denying that it is a significant inconvenience to passengers flying Emeriates/Ethiad/Quatar, but doesn't inconvenience passengers flying to the same destinations on US airlines and their partners.