Modern fighters are armored. In many ways, they're just as armored as WWII fighters. WWII fighters typically had self-sealing fuel tanks and armor plates in the cockpit. You'd be hard-pressed to find a modern combat type without those features. The external skin applied to the late war fighters was aluminum alloy as a general rule... you're just as aware of WWII aviation as I am (I assume as such), so I need not delve into construction techniques. Unless that fighter was something special like the Hs-129 or The Il-2, armor was more or less the same with the exception of magnitude in certain areas.
The rules of phyics and engineering apply to all things. Our understanding of these matters is what changes, not the actual forces. Again, you know this. WWII aircraft did not fly by a separate set of rules. As clearly evidenced by aviation design of that period, certain principles were not well understood. You just said the same thing. And so here I agree with you, that is why aircraft were often "overbuilt," which is never typically a bad thing, either.
Aircraft like the DC-3/C-47 are oddities much like the B-52 and military 707's: they last much longer than their designers intended them to. You could in fact say all of the listed aircraft are overbuilt, which is a neccessary element in the successfulness of their service lives. However, if we refer to WWII era aircraft, how many Ju 52s are still out there, or any of the other myriad commrcial aircraft? A tough aircraft is a tough aircraft, regardless of the era in which it was built... and a lot of them weren't nearly as tough as a C-47. Although the Ju 52 is not a great example: Axis aircraft weren't benefitted by being on the losing side, look at the Allied aircraft that were in fact "not-so-tough." A great many British aircraft were quite frail in comparison to their American counterparts. The toughness and strength of American aircraft was a defining characteristic in WWII, and few aircraft from the other powers could possibly hope to live up to those standards in general.
Kosh made a great point: WWII aircraft may seem to be so much tougher because they are not subject to the much more extreme forces a modern aircraft will be. That's already been noted beforehand. That does not actually make them tougher, though. Again, you cite engine power. That's part of overcoming the force of gravity and drag, but a thin pair of wings carrying over 10,000+ lbs of ordnance plus the weight of the aircraft still requires an incredibly tough structure. If engine power was everything, why don't we see a MiG-21 blasting off with a payload like that? The last '21's had almost 17,000 lbs of thrust at their disposal. Again, structure and aerodynamics. Too high a wing loading, too light a structure. But, it is by no means a weak aircraft. It is designed for a mission and does that mission; most WWII fighters were the same in that sense.
Lastly, how can you validate the "tougher" thing? Sure, those aircraft often operated in terrible conditions. I mean, terrible (of which you again are well aware). Referring to Kosh's question, modern aircraft can deal with like circumstances IF they are designed to handle it. Cold War Soviet types are a fantastic example. But, what about everything else? FOD. A modern jet wouldn't last in "Guadalcanal conditions" not because it isn't tough enough, but because the weight of modern systems and the tendancy of jets to suck up debris would make such an operation harrowing at best. For something like that, you really need something specail. The WWII fighters could also be compared to old automobiles. Sure they were MUCH more complex, but you could rip 'em apart in the field to service them, just like you could work on an old car in your garage. To continue the analogy, a modern fighter might be compared to a modern car. You can look under the hood to check things out, but you need special equipment to find out what's wrong and then fix it. Modern systems by virtue of the computer and other advanced technology are like that. The older planes weren't necessarily tougher, it's just technology has often gone beyond the good 'ol analog.