I can see how articles such as this could lead someone to think that US airports discriminate against trans people. But, keep in mind, this same exact procedure happens all the time to everyone. I travel frequently, and I see it.
Basically, it's like this: you get to the airport, get your bags and so forth situated at the desk, then you get in a very long line. You go through one or two clerks who check your ticket and ID. Then, the line splits off into one of several screening machines. As you get close to one, you empty your pockets, remove your shoes and your carry-on, and place them in plastic bins on the conveyor belt. When it's your turn, you step into the scanner machine, and it spins around you quickly. If you don't want the scan, the agents will instead do a quick pat down similar to what cops do. If there are issues with anything (by this time, someone else is already in the scanner), they ask you to follow them into a small room maybe 20 feet from the scanners. There are several rooms, and people are constantly in and out of them. I was taken to a room because they found "trace residue" on my hands (I had to do a random-pick hand scan). When in the room, there are maybe three agents in there with you. At this point, it would be good to say that you are transgender , since they do another pat down. They ask a few questions like where are you heading and where are you from. None of it is a big deal at all, since they do it all day every day to hundreds of people. It's not like they alert the whole crowd by saying HEY EVERYBODY, LOOK AT THIS!! After the very brief time in the room, they thank you for your patience, and have a great day. You then grab your things and go on your way. The whole things takes maybe ten minutes.
I'm not posting this to dismiss any issues anyone has had to face. I'm only doing it to say that all is not always what people claim.