A well reasoned article. Though I think Eben (aka Bike Snob NYC) has a tendency to jump straight into his core arguments without necessarily getting all his readers on the same page (hence the heat in this thread!)
I've done a lot of bike building, repair, maintenance, and comparisons, particularly in the last few years.
Up until 2000 or so, disc brakes did not exist for bicycles in a meaningful way. They were very popular on motorcycles, trains, and automobiles, largely because they provide stopping power for longer than the previous popular technology, drum brakes. And because they are arguably more maintainable than drum brakes, which are allegedly a pain in the ass to work on. Automobiles mostly moved to discs by the 50s or so; trains moved even earlier.
Bikes, on the other hand, had two (or three) competing brake systems prior to the 2000s. The most popular by far worldwide is rim brakes, the familiar clamping system that rubs pads on the rim of the wheel. These work great, are easy to maintain, and easy to fix when something goes wrong. Their biggest downside is wet, and even moreso muddy conditions, which can significantly reduce braking power when crap gets between the pad and the rim. And older cantilever brakes are really really tricky to set up, especially if you don't do it much. The 90s saw a significant improvement here with the development of Shimano's V-brake, which simplified rim brake tweaking to the point where basically anyone could do it.
V-brakes are essentially "good enough for anyone". But racers drive the bicycle part industry. Competition leads to the constant drive for new parts; companies sponsor top racers to get their parts on display at racing events; non-pro racers across the USA spend millions of dollars per year chasing incremental gains with these upgrades.
So racers moved to disc brakes. They were initially really heavy (they require attachment points and pad hardware that's much more substantial than the rim brake equivalents), really expensive, and not much of an improvement over rim brakes. Eventually folks figured out that hydraulic brakes (which use tubes filled with mineral oil instead of cables for actuation) could provide extra stopping power with less effort. And so all racing bikes adopted hydraulic disc brakes in the early 2010s.
Unfortunately, everything in the bike industry chases racing fads. There are only a couple of major parts manufacturers (shimano and SRAM) that make complete sets of brakes, drivetrains, and levers. This is changing with the recent growing popularity of brands like microShift, but most frame manufacturers have existing relationships with shimano and SRAM -- picture something like the Qualcomm domination in the smartphone SoC industry. And since those two big brands build racing and racing-inspired equipment, that's what we all get.
Most commuters do not need hydraulic disc brakes. They are an expensive luxury; there's no denying the stopping power is superior, but you don't need it if you're riding at 10-20mph across town to get to your job or pick up some groceries. As other commenters have pointed out, you're also fucked if something happens to one of your brake lines (aka oil filled tubes) because it's nearly impossible to fix on the road. That's a big downside!
Anyway, sorry for the rant -- the discussion here just really ground my gears because it's so similar to the flaws I see with our community when folks talk about technology or even finance: people don't acknowledge that there's context (and personal preference) involved with picking the right tool for the job.
Disc brakes are kind of like Kubernetes: great for heavy workloads, occasionally a pain, but overkill for the lighter workloads unless you enjoy geeking out (that's the personal preference bit). Rim brakes are more like running something on a Raspberry Pi: dumb for heavy workloads, but often a good price:performance ratio for lighter workloads.
I wish folks in our community would have a little more empathy and mutual understanding instead of constantly insisting that they're correct. I feel like HN used to be better about this, but I think this behaviour has crept in more and more since Reddit self-immolated.