Your second link doesn't show the total number of US air travelers, only passengers on US airlines. There are also non-US airlines serving the US. I'm not saying that this makes a very big difference, but it probably brings down the cost per screening to something around $10.
2nd Edit: Your first source already shows that "Aviation Security" only makes up 71% of the TSA budget, so that brings the cost per screening down further.
Edit: Found this number: "803.5 million scheduled passengers" From: http://www.travelpulse.com/dot-reports-17-percent-increase-i...
2nd Edit: Your first source already shows that "Aviation Security" only makes up 71% of the TSA budget, so that brings the cost per screening down further.