Shortly after the advent of the body scanners, the TSA was calling DEA and/or police whenever someone came through with cash.  They were told to stop that, and have pretty much complied.
I travel with cash as part of a business I am involved in.  Usually in the range of $25,000 to $50,000 or so.  I have been harassed twice at the security checkpoints.  The first time, a supervisor quickly corrected the agent, and I was on my way.  
The second time was more humorous.  I had gone through the regular metal detector, and had a pouch with a little over $25,000 in my pocket.  Alarm didn't go off, but the agent asked me what was in my pocket.  I responded "just cash", as I pulled out the pouch.  He asked to see it, so I unzipped the pouch and thumbed through the bills so he could see there were no explosives.  He then asked me how much money I was planning to "declare".  Two issues there.  First, you don't declare currency to the TSA, and second you don't declare money for a domestic flight.   Thinking he was just confused (it was terminal C at IAH and you can get to international departure gates from that terminal), I told him that I was flying domestic.  He repeated the same question.  I told him that I wasn't planning to declare anything since I am flying domestic.  He decided to just droop it at that point.  I was kind of hoping he would call his supervisor over.
Traffic stops are much more dangerous than air travel nowadays.  Especially if you have out of state plates.