Sorry this ended up a lot longer than I intended lol
I went back and watched through most of the first season, and I really do find it strange, it's like overtly left leaning text pretty often, but consistent conservative subtext. By that I mean they will have hodgins and bones saying "tax cuts to the rich instead of giving that money to poor neighborhoods like this so they stay poor, and minimum wage hasn't budged in 8 years, and it's even worse if you're an illegal immigrant." They'll talk about people being gay and just treat it as normal but don't ever show it on screen(I would say this is neutral/a little positive?). Bones likes rap music, they're constantly asking "are you threatened by working with a woman?" and she knows martial arts and self defense and shows it off very regularly. Angela is very independent as well.
But at the same time, bones is consistently showing needing support from booth and angela (hardly ever the other way around), women are usually dressed in pretty revealing ways (angela and bones pretty consistently wear low vnecks), one episode someone plants a carbomb and they think it's a muslim, then pretend "how dare we think it was a muslim" and then it turns out it's his brother who is also muslim and says he did it for his god? Every time Booth mentions christianity it's seen as positive and heartwarming for him or people he meets, and bones even becomes the damsel in distress and Booth has to rescue her, which makes all her punching and fighting seem irrelevant.
It's very weird it feels like it's all plausable deniability where they could say that's just what we wanted to write an episode about (other than the Booth is a strong man who cares about real american values) I didn't even realize they explained away brennan's autistic coding by saying it was her upbringing, like that's the only way someone could be like that (or with the autistic kid being autistic only because he's >160 iq, otherwise he'd be normal).
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I think the only things I would disagree with is, Bones didn't become rich by pulling herself up, it was just because she worked as an escape, and then I think the writers just wanted to show that she is successful in everything she tries because she's just awesome that awesome (possibly conservative coding?)
I would also say Bones feels in charge half the time, even more in charge than the administrator really. She'll ignore Booth and all the laws and all the rules and do what she thinks is right, and then Booth usually ends up following after her (to protect her of course). The Administrator started off as above everyone but later in the season it feels like he's their colleague who deals with the press and tells bones that she has to go with Booth sometimes. I think if you replaced him with a woman no one would really notice unless it was in the first few episodes. I also think Booth isn't quite a perfect conservative American, maybe a perfect soldier, specifically because he will lie to people, do the wrong thing, etc, but it's what his boss told him to do. At least that's what it seems like, the writing for him and Bones are probably the most inconsistent in the whole show. Also the autistic kid, I think it literally was just the writers wanted to kill off a main character, and so they just decided on him because it was easy. To be honest if I was the writer I would've done the same thing, most episodes it feels like he doesn't add anything unique or interesting, just a "look I'm smart." Lots of interesting stories to tell with an autistic character, but if they don't know how to tell them and it makes the character unpopular, time to get rid of him I guess.
Other than that I think you pretty much nailed it, I just wanted to say that I found pretty often the show is surprisingly progressive, just maybe not in the subtext of the show. It's just such a weird mash-up of "look how progressive we are, we have a badass woman, the guy is getting bossed around" that somehow turns into "the strong man learned to do the right thing and also saved the woman." I think since Booth is always in focus and always showing he's a strong conservative man, they can get away with saying whatever they want, because the progressive words don't matter, what matters is how it feels. (Note this is all based off season 1, later seasons they definitely lean in to what the fans want and a lot of conservatives were definitely watching)
This is 100% not true as I have personally had several times where I got ransomware (though still the thing I wanted to download somehow?) in late 2000s / 2010s. Hasn't happened a single time since, even downloading the most sketchy torrents. For a lot of younger people, if they want to torrent something they're not looking at trackers or much of anything, they just want the download. Windows defender used to be complete trash at preventing viruses so you'd need to know to download things like malwarebytes and be a lot more wary of what you download, and even if the torrent is 100% legit you'd have random registry/driver/software issues. Now these issues are rare unless you're downloading some custom software or a much older game.
The one thing I would say was a lot easier back then is it would say "xyz free download" and it actually would be the thing itself instead of random bloatware.