Why should anyone be putting their legal rights aside? Or are you suggesting that now that someone staged a(nother) terrorist incident on US soil that habeas corpus is an quaint, antiquated ideal?
They sure do. They also have the right to NOT FLY. If they are made uncomfortable they have the right to not fly. They also have the right to look away or change the station on their radio/tv if they don't like the content. Sadly, they choose to harass/bully their way through things, projecting their views onto others rather than shutting up and moving on.

The proble is that if a bunch of people said to JetBlue that they were uncomfortable flying and wanted to switch flights to one without an arab on it JetBlue would have all sorts of scheduling issues, so they did their best to accomoodate everyone. And in doing so they violated this man's rights. Sad, but true.

The post-9/11 world isn't so much different than the pre-9/11 world, except that the US has gone out of its way to make people hate us more than they used to. One event should not be used to justify wholesale ignorance and/or suspension of civil rights.