The $10,000 rule was actually drawn from Federal law prohibiting carrying more than $10,000 in cash or negotiable instruments into or out of the U.S. -- it is derived from money laundering legislation associated with the Bank Secrecy Act. It does not apply to travel inside the U.S.
The TSA directive idenitfying large sums of cash is not designating the cash as contraband as an "indicator" of criminally suspicoius activity. As such, the large amount of cash alone should not trigger questioning, however a large amount of cash in conjunction with other indicators is what is supposed to trigger questionning and the filing of a suspicous activity report.
What amount is a "large amount" is discretionary in light of the totality of the circumstances (i.e., what other indicators existed.) I would guess this case was a training and supervision issue -- the TSO did not have sufficient trainng on suspicous activity reporting and the supervisor didn't monitor the TSO's activity.
LEO's are typically much better trained on these issues. Confronting the TSO will only cause more grief. If you want to get through fast, simply give a logical explanation -- I'm giving the money to a son/daughter to help with them with a down payment ona house; I'm hoping to buy (some expensive gift) for a spouse; My credit cards were stolen and I'm using the money for travel expenses, etc. If you have time and want to challenge the TSO's authority on this, call a supervisor and/or LEO