When a starry-eyed high school graduate with little knowledge of how the world works, but with a strong interest in and ability to do science, goes to a top research university, he gets a lot of that academic bubble viewpoint. He's not taught to think independently or to identify and question the fundamental assumptions of that bubble. So he just takes it all in and does "the right thing" to go on to get a PhD, without necessarily thinking about all the implications for how it determines the rest of his life.
Doubly so if he comes from a cultural background that puts academic achievement and degrees on a pedestal. A lot of Asian cultures, for instance.
I don't know if there's a top-down solution for this. Any institution will be blind to the fact that it isn't able to look at the big picture of reality with minimal bias. It is really up to those of us who are aware of these issues to talk about this on the internet, and hope that as more people use the internet, curious individuals can learn enough to make a good decision.
BTW, the above description is based on myself. I am Asian American, had a sheltered suburban upbringing, really excelled at math and science, got almost full scores on college entrance exams, went to college at a top research university, etc. This university was really geared toward pushing people into scientific research. Fortunately I wasn't good at research but was great at building things, and realized early enough that I should go into industry. I've learned so much more about the world since then through my experiences outside of academia.