Hi Seachain,
There has been quite a bit of discussion on this topic over in Travel Safety/Security. Search on "shoe carnival" or "shoe harassment".
The short answers are:
1. The TSA has the authority to search you in any way it likes before allowing you to pass the checkpoint. Supposedly you can refuse the search at any time and get a refund for your airline ticket, but scuttlebutt has it that you can also be arrested for the "suspicious behavior" of refusing to consent to search after you've entered the checkpoint area.
2. Refusing to remove your shoes is not supposed to automatically guarantee you the full secondary wanding. If your shoes don't beep, you might get a secondary search if your shoes fit some profile like having high heels.
3. At some airports (notably SEA, DFW and some terminals of EWR) there is a shoe carnival, by which we mean that everyone gets secondary as a punishment for refusing to remove shoes, regardless of heel height. This is not standard operating procedure. The TSA says this should not happen. Still, the TSA makes its own rules and apparently doesn't have to follow them. If you question these shoe fetishists they'll give some nonsense excuse about why you got sent to secondary.
4. Some TSA apologists claim that searching or x-raying shoes that don't beep is necessary to find hidden non-metallic material like that Richard Reid had in his shoes. Don't believe them. An equivalent or larger volume of non-metallic material could easily be concealed in a body cavity and we don't search those. The real point of shoe carnival is to make us feel safer, but it doesn't make us any safer.