When I go through TSA I insist on holding my wallet in my hand when going through the scanner. Some airports said it is against their regulations (for example MKE). When they do that I file a complaint (ask the TSA supervisor they have a form for it).

I have precheck, and now that they've expanded the program it isn't really an issue for me.

Bottom line - don't let the TSA let you get separated from your wallet. If they insist on it - complain.