Dragon's secret of course, is that she's human.
Yes, Dragon is still a bundle of wires instead of a bundle of organic neurons, but she comes from the first half of Worm where the development of characters is humanist. We get her perspective, and it's a believable, reasonable, complex, even sentimental perspective.
Hell, she has a girlish crush on Armsmaster. (It's interesting how Worm uses "unfulfilled romantic desires" as a way to humanize the monstrous-appearing female characters. There's Dragon, there's the heartbreaking scene with Sveta and Dr. Yamada, there's epilogue Bitch, etc.) There's all sorts of details and aesthetic stylings that portray her in a human light.
In contrast, the actual inhuman characters are more like Glaistic Uaine, Eidolon, Scion, Contessa, the international villain teams, Ziz, and Khepri. We can far more empathize with Dragon, the AI, than we can with those freaks.
Dragon even takes a spin on the idea that we need to place unbreakable bonds on an AI so it doesn't take over the world, by asking "okay then, what should she be yoked to? Oh, the government. That's great." So we're tormented by this image of a very human person who has the power to do good, forced to do evil by a stubborn or malicious government. This is extremely powerful in the scenes where Canary is introduced to the Birdcade, and where Dragon and Defiant invade Taylor's school. It's reminiscent of the oppressive Superman in Frank Miller's "Dark Knight Returns", though even scarier because even the possibility of rebellion is ontologically foreclosed.
(It's less powerful in the scenes with the comicly inept Saint, but we'll discuss how that thread works on a future date. Suffice it to say, watching her wrestle to throw off her bindings against him is the truest moral ambiguity in Worm.)
So far this is pretty good stuff. It's made literal in the text when Defiant discovers that she had a trigger event too. Oh, also when they have sex.
But the value of reading a fully realized AI character only goes so far (about as far as Crystal Society ). Dragon goes a little farther.
Because Dragon is still a god.
As far as humans go, Dragon is a pretty good one. Beyond simply being on the side of the "good guys", she clearly has an instinctive sympathy for the lowest and outcasts. It's no coincidence we first get her point of view while she is guarding and growing to love the prisoner Armsmaster. In combat situations she goes to extreme lengths not to unnecessarily hurt a villain. She sees an innocent person being thrown into the Birdcage so she... writes a letter to the judge asking for mercy. Refusing is impossible, and she can not see beyond the idea of the Birdcage existing, so she does what little she can within the system and acts like what we would consider a mature, responsible adult. And even aside from the innocents, she tries to organize life in the Birdcage (which she runs) so as to reduce their pain and death.
Right, not only does Dragon provide a lot of the best technology the PRT can use, not only is she the most omniscient and ubiquitous fighter in major combat scenarios, she also runs the parahuman prison system - the Birdcage. And let's call it what it is.
Dragon runs Hell. There, she is the ultimate authority, who Created it and manages its every detail.
Now this is where Worm made a really interesting decision. Superhero stories all the time have the concept of "the jail where villains are kept" that go hand in hand with "the jailkeepers are terrible." Sometimes they are inept and easily seduced into villainy, such as at Arkham Asylum. But most often they are depicted as sadistic Nazis who enjoy tormenting their prisoners, and using them to punish their political foes. Captain America: Civil War is a cliche example of this. The moral complexity here is to make us sympathize with the prisoners, and doubt the morals of the people who choose to run such institutions. (In the more nuanced examples of this, running a prison turns good wardens bad, a la the Stanford Prison Experiment, but usually the lesson is just that "this prison warden was bad and should be replaced with a good person.")
In Worm, the Birdcage is run by a good human, who has no sadistic tendencies towards the inhabitants and works to alleviate pain and suffering as much as she can, and has enough awareness and power to do this without relying on any fallible guards.
Dragon, to the universe of the Birdcage, is a materialist god. A superior being with infinite power who aims to reduce material suffering. She is basically what would happen if you put your favorite rationalist tumblr in charge of a suffering world.
Such a person is still human. They can not see beyond "working within the system" to question the existence of the Birdcage entirely. (To the reader, of course, it's clear the Birdcage is going to be destroyed from the first time we see it.) They can try to mitigate the crises within the dysfunctional world, but they can not change its function.
And, because of this generous treatment of Dragon, we can't blame the evil in the Birdcage on "bad guards" or even "stressed human beings." A prison is just a hellish place to put a person, no matter what, and the society that does it needs to own it.
Such a characterization contrasts heavily with say, movies about Robocop where because of his mechanical parts he transcends humanity and can enforce the morality he is programmed with onto rich and poor alike.