Well, just because this topic bugged me, I did some research last night.
First, there is a distinction between "what the rules say" and "what has been proven to be dangerous through scientific/engineering analysis." The bottom line is that, regardless of the science, the FAA rule is clear as day: Don't use transmitting devices in a plane. If you want to dispute the need for such a rule, then go get a Ph.D. in electrical engineering, go write a paper, and then convince the FAA/FCC/airline industry to change the rule.
(I think this is just a special case of one of my biggest pet peeves when traveling, or really in general: People who simply cannot follow the fucking rules. Oh, the seatbelt light is on because of heavy turbulence? Sounds like a good time to get out of your seat, force the guy in the aisle seat to ALSO undo his seatbelt (that's usually where I'm sitting), and open up the overhead bin to get something meaningless because, you know, those lights don't mean anything.)
Second, most of the papers/articles dealing with aircraft systems interference that I saw had to do specifically with cell phones, not with Wi-Fi networks. Although I don't work in the field of EMI engineering, I do know that it's a critical issue with some of the systems that we build...which go on airplanes. The fundamental problem is that, in order to definitively say that EMI won't be a problem, you have to conduct extensive testing...which is involved and expensive. If you haven't conducted that kind of testing, the best you can say is that you haven't certified your system. In engineering, you can't deliver something with a guess, even if you THINK that EMI wouldn't be a problem. I strongly suspect that the airplane manufacturers are simply being conservative since they haven't done the testing, but I'm not even sure that a comprehensive testing plan would even be possible -- how could you possibly anticipate all of the possible configurations of emitters on a plane?
Finally, EMI is a complex situation, and although it would seem unlikely that an individual device would affect a critical airplane system, the interaction with other emitters and the environment might have some kind of effect. Again, without testing, the only thing you can say is that you haven't confirmed there won't be a problem...and since we live in a lawsuit-crazy society, it's understandable that they want to be cautious.
And yes, if a terrorist organization had detailed information about airplane guidance systems, you could imagine that a specially-designed transmitter could wreak some havoc. Heck, a portable EMP generator would do the trick -- given how most jets are fly-by-wire systems, I would imagine that taking out the control systems would make it difficult or impossible to land the plane safely.