Seems to me that your positions are in opposition to each other.
1. There’s a traditional visual language that people instinctively prefer.
2. Modern architectural sensibilities have superseded traditional visual language through repetition.
I’m reading this to mean something like “people like their own traditional foods but since they've been drowning in pizza for the last 70 years, they’ve forgotten about their traditional foods.”
How can a basal, instinctive preference just disappear? Can the sex drive disappear with enough brainwashing?
I'm not claiming that people instinctively prefer anything. I'm saying that they've been socialized to believe that "traditional" architecture is some indicator of societal excellence. I don't think its weird that people report a bias they've been taught to have.
The article even seems aware of this possibility when it mentions that architecture students prefer modernism (with the semi-covert implication that their education is poisoning their aesthetic sensibilities). I claim its at most partially because they've been taught to prefer modern designs, but mainly because they've been taught to think about visual languages consciously, so they are able to recognize what a given architect is trying to do, in a way that a layperson might not. That's certainly why Thomas Kinkade gets as much hate as he does (that and the dodgy business practices...).
I'm also not claiming that people have been starved of traditional architecture entirely, just that nobody is building things in the traditional style now. They're not tearing them down either, the White House East Wing not withstanding. This is a novelty bias, nothing more. If you only ever see neoclassical architecture in buildings that are designated as "fancy" or "special" or "august", and all these modern, ordinary buildings do not, you're going to assume that the style itself, and not simply the age and intent at construction are what contributes to that.
I mean, 39 out of 50 US state capitol buildings have domes, as does the nation's capitol building. I think anybody in the US can be forgiven for thinking that dome = legitimate seat of authority. Certainly, that was the hypothesis behind the design decision.
Speaking only for myself, I found Washington DC, which is all neo-classical all the time, just really boring. All the buildings look the same, and I couldn't escape the sense that I was in museum that hadn't been updated in a long time. Chicago's Fields Museum has the same quality.