This brings up a point that's been bugging me for awhile. Why does the design of a civilian passenger jet give the pilot the power to turn the plane's transponder?
In common with most aircraft "black boxes", you need to be able to turn it on and off (or into standby at least) in case it fails. It's also a way of positively making sure that the kit is on - much of this kit could probably be automated, but crews run through checklists to ensure a) that a system is on b) that it's functioning, and c) both crewmembers are aware of the status of a system and record it in some way.
Added to this, there are multiple "modes" for the transponder for different circumstances, so you need to be able to select any one at any one time, which naturally enough involves having the capability to switch off one or more of them. I think you also need to manually enter the code requested by Air Traffic Control - perhaps these codes could be delivered from ATC to an onboard computer rather than over radio, but again it's probably about positive procedure designed to make sure everyone knows what's happening with what.
The simplest reason is "why not"? At least until 9/11, it wasn't a major issue to consider. To make it tamper-proof it would need to be ultra reliable and redundant, and you'd have to isolate it from any controls and bury it in the airframe somewhere. Or use some sort of security lockout to access the modes. In the scheme of things, that's a lot of effort for possibly little potential return in terms of successfully dealing with hijackings. And I don't know, I'm no pilot or engineer. Maybe it's being looked into? But you might just as well ask why many other systems aren't automated and locked out - reliability, serviceability and cost are probably the main reasons. Aviation types don't like to remove the human from the loop unless it's truly safe and cost-effective to do so.
You could do worse than sign up to
www.pprune.org and post a question in Tech Log, though they will probably assume you're a CT!
ETA - you also have to consider that lack of response to radio calls, being out of position, and dicking around with the transponder, are all signs of trouble. If you have the transponders somehow automated, that's one warning sign removed.
ETA again - this pdf has an interesting comment about transponders perhaps being viewed legally as "defective" for being possible to turn off -
http://www.fed-soc.org/pdf/Collateraldamage.pdf - I think this is just brainstorming by a legal type who doesn't know the technical details (not that I do very well!).
