I just had my first experience with the body scanner a couple of weeks ago in Amsterdam, and I'll be honest, it wasn't terribly enjoyable. Nor was being randomly selected to go into the "holding room" and be patted down on Sunday at the MSP airport. I know it was just a random selection - the (female) TSA agent who selected me even called me "honey" when asking me to step aside (in a nice, motherly sort of way, not a sarcastic, demeaning or creepy way). But still, I felt a bit insulted to be randomly selected. But I can see that both are necessary.
The body scan was fine except that they just told me to go in the cylinder and hold up my arms, but they never told me for how long or instructed me that I could leave, so I stood there standing with my arms up like an idiot for longer than necessary.
It's uncomfortable but really I don't mind. We do need to do our best to keep air travel safe.
Interestingly, the same people who feel their personal freedom is being violated by the body scanner are the often same people who are on board with the war on terror and harsher immigration laws as a result. Sometimes the same people who admit to feeling uncomfortable being on the plane with Muslims dressed in traditional clothing. You can't have it both ways - if you're scared of seeing Muslims on your plane, you should be thankful for the body scanner; if you want your own personal freedom, you should want all innocent people to have their personal freedom and not be subject to profiling or harsh laws formulated with the guilty in mind.
EDIT: I better just go ahead and say that I'm not accusing any specific people on this forum of the attitude I describe in the paragraph above. It's mainly other people I've observed/overheard at airports.