First, it's not just an "honor system," as there is generally at least some effort at enforcement on the part of the flight attendants. I have personally had the experience of having a flight attendant ask me to put away my kindle because I wasn't paying attention to the announcements.
As I've explained elsewhere in this topic, aviation mishaps are almost always the result of multiple factors, where if any one factor had been removed the mishap would not have occurred. "Passenger with unauthorized active RF transmitter" could be one source, but it's probably not going to cause a mishap alone.
In aviation we define "risk" as a combination of probability and severity. You can drive down the risk for a particular hazard by either lowering the probability or lowering the severity. The only way to completely eliminate risk is to not fly, so every flight involves accepting some level of risk. It's really a question of residual risk you're willing to accept balanced against the costs (financial and otherwise) incurred by attempts to further reduce the risk. Several people in this topic have discussed the costs of just the current system of having everyone turn off their phones during critical phases of flight, and complaining that the FAA doesn't apparently care about such things. I disagree with them--if the FAA truly didn't care, they would do exactly what you say: confiscate all electronics at the gate and lock them in a shielded box.
>It just strikes me as odd that failure to pass an EMC SOFT grounds the plane until the issue is debugged, but then they just allow an random passenger to bring any random radio aboard just so long as they promise/remember to turn it off during critical phases of the flight.
Keep in mind that I'm flying in a developmental test environment. That means that we're dealing with a lot of stuff that has never flown before, or are using it in ways it has never been used before. Because of the nature of what we're doing, we already have a lot of risk baked into our flights that an ordinary flight does not have, so we tend to be a lot more conservative about the risk factors that we can control.
[EDIT to add quote for context]