I don't think Netflix qualifies as in-house programming. IMO, when Joel refers to in-house programming, he refers to companies that have a core competency that has nothing to do with software.
If you work at an insurance company or tech support company, you'll be writing code to make lives easier for people who work at the company. Your customers are in-house employees.
Some companies really do see their in-house programming as critical for success, and treat it accordingly. I get the impression that NetFlix, for instance, is a pretty good place to be a developer, because the company sees logistical software (for optimizing DVD delivery) as a critical components in winning against blockbuster (they also do video downloads, from what I've heard, but that's so close to an actual software product that I'm not sure I'd call it "in-house"). I gather that Amazon is also pretty innovative, but I don't know anyone who works there.
On rare occasion, product companies are clueless enough to treat their developers like typists - I've been at exactly one. The difference, of course, is that these companies don't really last long. A textiles company with crappy software management practices can survive anyway, whereas a product company with that attitude will almost certainly fail, and quickly.
So in general, I agree - though there are some notable exceptions.