I don't much like the post, but a charitable partial reading would be something like: I feel left out of / alienated by hacker culture because, although I'm a programmer by trade, their culture isn't really my culture. It wasn't phrased like that, but it is a fairly common sentiment in a lot of fields.
I even have it somewhat in mine, though it's more of there being multiple cultures and me being part of a less-dominant one: I research AI in videogames, but am not really part of "gamer culture", though I do play and study games extensively. I just tend to prefer playing and analyzing more simulation / indie / art types of games, and historically important games, and don't really keep up on recent AAA titles or feel part of the Penny Arcade / Kotaku culture. Sometimes that leads to awkwardness if people expect that everyone who studies videogames is "a gamer" in that cultural sense, so I could see a way that there could be programmers, even good ones, alienated by hacker culture if they feel it's assumed they'd be part of it, but they aren't.
I knew people like this. I worked in a database consultancy full of them. They eventually drove me out, because I couldn't connect to them on any level. They had no excitement for computers, or technology, or anything they did. They had a job, and they did that job (usually poorly, but the two boss guys were legitimately good at what they did, so were able to set out the database schemas and such so nothing got too fubar'd later on). They're the sort of people who say "a job's a job" and can sit at a desk from 9-5 doing pretty much anything as long as a pay check arrives.
What surprised me about people like this is that I always ascribed the ability to do a job in that manner as something that required a lower intelligence quotient: you had to be OK when presented with broken processes, manual tasks that are easily automated, and have little real pride in the product you produce. I thought this sort of stuff would drive reasonably smart people mad. But here they were, reasonably smart people, who just didn't care. They were all a product of CS when it was the "money" degree, like BioChem is now. The smart choice they made was "If I don't give a shit about any job I could possibly do, I may as well be paid decently for it." The author even says "I also have no idea what job I'd do otherwise," even though he clearly dislikes what he's doing.
The author is alienated because he doesn't give a shit, and he's found himself in a position where that isn't status quo. A lot of the posts here are surprised he's got this far; which I think shows HN's fairly biased population. There are loads of programmers who don't care. They aren't working in the Valley at companies you respect, because to be talented enough here requires passion (he seems to indicate he's in the Valley, but that doesn't mean he's at a company you respect ;) ) But someone, somewhere is coding crap bespoke software, and all those CS grads that aren't in the Valley are getting hired by someone. It's easy to forget all these people when you live in hacker communities like the Bay Area, Portland, NYC etc.
I even have it somewhat in mine, though it's more of there being multiple cultures and me being part of a less-dominant one: I research AI in videogames, but am not really part of "gamer culture", though I do play and study games extensively. I just tend to prefer playing and analyzing more simulation / indie / art types of games, and historically important games, and don't really keep up on recent AAA titles or feel part of the Penny Arcade / Kotaku culture. Sometimes that leads to awkwardness if people expect that everyone who studies videogames is "a gamer" in that cultural sense, so I could see a way that there could be programmers, even good ones, alienated by hacker culture if they feel it's assumed they'd be part of it, but they aren't.