The first thing however, that you need to realize is that air travel is not your right. While you have many rights to be secure from intrusion within your own home, you waive many of those rights when you step outside. You can walk buck naked through your living room, but you cannot do so on the street or in a public park. You can stare a photo of your worst enemy, lie about them, tell them that you hate them and tell them that you wish they were dead, but if you do so to their face, you may get into trouble. If you happen to live on a private road, you can drive as fast as you like, but as soon as you enter a public street, you must obey the traffic laws. You have the option to move around on foot, by car, by rail, by bus or by private plane and so as difficult as it is for some people to accept, air travel is a private decision that you can opt out of by choice. The farther you step outside of your rightful sanctuaries, the more you waive your rights.
The second thing that you must understand is that commercial air travel does not occur in lanes which are considered to be public throughways. This really has two parts: The first part is the airplane itself. You have limited rights on an airplane because you are actually just inside a vehicle of sorts, that is owned by a company such as Delta, AMR Corp or United. The government does regulate many of the safety standards that must be adhered to when you are on the plane and it has a substantial amount of jurisdiction, but the plane is still owned by a company, it is theirs, and they can choose whether or not they want you on it [with some restrictions]. The second portion to this is that by choosing to travel through a commercial air company out of an airport, you are surrendering certain rights to the government. Specifically, you must show IDENTIFICATION, you must be willing to submit to unwarranted searches, you must be willing to have your luggage inspected (which is why you must put a TSA lock on your luggage or the TSA can cut your lock) and finally, you must be willing to be screened before you step on board the aircraft. Once in flight, you remain in a private vehicle but under government control and while the airline submits a flight plan, the government has complete authority to modify it. By choosing to fly, you waive certain rights and if you do not want to waive these rights, you have the option not to fly.
One caveat to this is that you do have rights to be treated with fairness, with dignity and without discrimination by the government. To this end, portions of your air travel which involve the government, do entitle you to feel that you are not being taken advantage of. However, the government realizes that air screening is intrusive and for this reason, they continually upgrade their training systems to minimize this. They are not perfect, but they do try quite hard and the number of cases of unfair treatment by air passengers is quite small.