It probably has a lot to do with the fact that people bought them in droves when new. They were the best selling SUV for over a decade. The numbers destroyed in the program were a small fraction of overall sales, and being drivable and continuously registered for at least a year prior were also requirements.
It's not luck, they are generally good vehicles if they are maintained and not allowed to rust out. Sure they've had issues, so has every other SUV ever built. It seems like the merits of the 4Runner in these threads are always based on bashing everything else as junk. 4Runners are good SUVs, but the prices of some used ones are pretty ridiculous no matter how reliable they are. There's a 2000 plain jane steel wheel SR5 on Craigslist for $13k with 121k miles on it. That's just crazy. They aren't all priced like that, but it's hard to find one that's a good value. That doesn't mean they are bad SUVs, but the prices are a bit over the top right now.
For what it's worth, Bronco II prices are insane too. People pay 2-4x as much as a first gen Explorer for something less capable, less comfortable, and less reliable. That's proof that some of these Radwood era prices aren't just based off of people making strictly practical choices.