It's not that people "haven't learned to think". It's that their perception of reality is driven by their ego.

It must be understood that this is the case with all mentally competent people. An ego's appetite can be trained and controlled, but generally speaking, everyone wants to see themselves in the same basic, overwhelmingly positive way.

When an "empiricist" comes into the fray, they've trained their ego's appetite to prefer circumstances that allow themselves to be on the side of "hard data", "scientific consensus", or, as you've put it, "academic orthodoxy". Thus, the empiricist will dismiss theories that seem to be "outside of the orthodoxy" and ridicule their purveyors/supporters/believers.

This is your ego operating to give you the room to feel superior and keep your self-image adequately positive. The same thing is happening in your friend who has the quantum healer machine. They see themselves as someone who is able to spot frauds even when many other people cannot and use this information to their advantage (something you have in common).

Most likely the key difference here is the amount of trust each party has learned to place in secular/technological/academic institutions. You believe you can see the fraud perpetrated on the public by exploitative marketers and snake oil salesmen. They believe they can see the fraud perpetrated on the public by exploitative elitists and the corporate upper class (that's currently suing them for an unpaid medical bill).

The truth is that both perspectives are sometimes valid. "Learning how to think" is learning how to recognize your biases and think about an issue from a neutral, dispassionate perspective, without discounting any potential argument without consideration.

It's never too late to learn that, but most people have internalized their emotional disdain for "the bad guy" that they believe is oppressing them, whomever they assume that is, such that they'd rather make up a justification to discredit the other side's arguments rather than admit that they're potentially, though not necessarily, reasonable. And while overriding this impulse is a great skill to practice, it must be understood that very few people will ever do so to an extent that makes it usable.

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The key to understanding people, IMO, is recognizing that human decision-making does not operate on objectivity or observation, but rather on the unavoidable and undeviating need to see oneself as intelligent, aware, and discerning.

People must see themselves as important and significant to justify their existence. This is true of all people; it's part of human self-preservation. Do not believe there are exceptions. Most people don't like this explanation because it implies that their self-importance is illusory, which funnily enough, really only reinforces its correctness.

The way to control your ego is to train it to value the right things as signals of importance.

If you want to change someone's mind, you must not argue that their conclusion is incorrect; rather, you must discover what biases and emotional mechanisms are at play in shaping the perception that leads them to that conclusion.

Once you accept this, the world is much easier to understand, social situations are much simpler, sales and marketing become both much more practicable and much easier to notice, and a lot of bitterness and antipathy goes away.

Disclaimer: I have no research or supporting evidence, this is pure conjecture, and there is no reason at all why you should listen to me.