I think you're mostly right about the "Hulbata" theory. I don't think audiences had to be disaffected per se but the first Matrix is high concept in all senses of the word; it's asking philosophical questions and much of the diegetic worlds it builds are hypothetical - sketched in, as a sort of framework for the bigger questions. A hell of a lot of gimmes that didn't really matter.
Add that to the peak late 90s style and what were cutting edge fx and it was really new.
But you're right, because of that we could project whatever we wanted into it. But then the sequels were fleshing out and codifying it all and making more laws and rules, and it became too literal. Zion was an ideal of humanity in the first film... in the second film it actually appears, and it seems to be a kind of irritating drum-hippy dance party.
If the first movie had you thinking about, I dunno, Baudrillard or something, then you meet the Architect etc and it's suddenly a lot more like Jainism meets the Masonic lodge, whether you like it or not.