A revisionist counter-narrative has sprung up in many places on the internet, propelled in part by the popularity of games like Warthunder. The B-17, this narrative goes, was no more rugged, survivable, or defensible than any other bomber. Photographs, reports, and veterans' accounts of B-17s landing with exceptional battle damage are dismissed as rare exceptions. Instead, the loss rates of B-17s in late 1943 are used to prove the vulnerability of the platform to fighters of all stripes.
I find this difficult to square with an interview I conducted earlier this year with a surviving B-17 pilot. While admittedly no expert on WW2 aircraft design, I know enough to ask interesting questions; and this gentleman spoke convincingly of the ability of his B-17 to repeatedly absorb hits, aided at least in part by a design philosophy that stressed redundancy - ie, two cables leading to the rudder, so that if one was severed, the co-pilot could still fly.
This is an interesting question that's honestly a lot harder to answer than one would imagine. On one hand, there are numerous losses and on the other hand as you mentioned, there are many circumstances where planes sustained extensive battle damage. This extends to P-47s, P-51s, and plenty of other planes in WWII.
To that I'll say this, aerial combat damage is honestly an incredibly difficult thing to quantify. Because there are so many instances where critical failure can occur (explosive shells, flak, sudden structural failures, etc) but don't, a lot of it is honestly down to chance and luck. That said, with regards to the B-17, it was indeed a rather rugged plane. The only problem of course being that when it was hit with high explosive shells repeatedly no amount of redundant systems could ostensibly save it. Provided the shells hit areas where critical damage would prove fatal.
Further more we have to try to understand aerial gunnery. Which at the time generally was rather inaccurate. Combine this with systems built for redundancy and it's possible to see why many planes managed to survive rather severe damage. Even so, the B-17 formations were not without merit. Even though there were very high losses, simultaneously, the German fighters which engaged the B-17s suffered massive losses as well.
Loss rates aren't a good measure of robustness; planners rapidly adjusted missions to compensate.
Freeman Dyson mentioned this in his memoir of doing operations research for the RAF; here he is discussing how hard it was to adjust for these choices (the same problem that internet experts apparently have):
My job was to see from the results of many operations whether MONICA actually saved lives. I had to compare the loss rates of bombers with and without MONICA. This was difficult because MONICA was distributed unevenly among the squadrons. It was given preferentially to Halifaxes (one of the two main types of British heavy bomber), which usually had higher loss rates, and less often to Lancaster bombers, which usually had lower loss rates. In addition, Halifaxes were sent preferentially on less dangerous operations and Lancasters on more dangerous operations.
http://www.technologyreview.com/article/406789/a-failure-of-intelligence/page/4/