I did check with the TSA for their tips before writing this article, but I did not find their suggestions very helpful or, in reality, executed with consistency. In practice, I think approaches vary from airport to airport.
Some airports are starting to have "practice runs" designed for kids with autism, so you may want to ask about that in advance. I think it's a great idea.
In my experience, going through security screening, with or without a child, is not fun, but keep your cool. At the security gates, consider the handicapped entrance, which may cut your wait in line.
Since the alternate security check for handicapped individuals tends to be more physically hands on and thorough, you can ask the checker to touch your child as little as possible, but they might not comply. Expect them to check your child's wheelchair or stroller. Being touched by a stranger may not be comfortable for your child, but if you prepare them in advance with visual helpers and simple explanations, I have found that it helps a lot.
At the gate, ask to seat your child before the other passengers board the plane, if needed.
As you board, warn the attendants that your child may vocalize or squirm.
I do find that an upbeat and loving attitude (rather than appearing anxious or embarrassed) earns me more tolerance for him--I've never been hassled about my son's behaviors on the plane (and he does flap and vocalize, sometimes).
Legal disclaimer: The tools and recommendations on this website are not intended to replace the information, training, and support you may receive from qualified medical and therapeutic professionals. It is the parent's responsibility to verify the accuracy of recommendations and information before implementing changes that may impact the parent's child.