Thanks for comments. What I wrote was exaggerated, written under strong emotions, when I realized that the whole phyg discussion does not make sense, because there is no real harm, only some people made nervous by some pattern matching. So I tried to list the patterns which match... and then those which don't.

My assumption is that there are three factors which together make the bad impression; separately they are less harmful. Being only "weird" is pretty normal. Being "weird + thorough", for example memorizing all Star Trek episodes, is more disturbing, but it only seems to harm the given individual. Majority will make fun of such individuals, they are seen as at the bottom of pecking order, and they kind of accept it.

The third factor is when someone refuses to accept the position at the bottom. It is the difference between saying "yeah, we read sci-fi about parallel universes, and we know it's not real, ha-ha silly us" and saying "actually, our intepretation of quantum physics is right, and you are wrong, that's the fact, no excuses". This is the part that makes people angry. You are allowed to take the position of authority only if you are a socially accepted authority. (A university professor is allowed to speak about quantum physics in this manner, a CEO is allowed to speak about money this way, a football champion is allowed to speak about football this way, etc.) This is breaking a social rule, and it has consequences.

Every self-help book (of which there's a huge industry, and most of which are complete crap) is "trying to change the way people think", and nobody sees that as weird.

A self-help book is safe. A self-help organization, not so much. (I mean an organization of people trying to change themselves, such as Alcoholics Anonymous, not a self-help publishing/selling company.)

The Khan academy is challenging the school system, and nobody thinks they're phyggish.

They are supplementing the school system, not criticizing it. The schools can safely ignore them. Khan Academy is admired by some people, but generally it remains at the bottom of the pecking order. This would change for example if they started openly criticizing the school system, and telling people to take their children away from schools.

Generally I think that when people talk about phygs, the reason is that their instinct is saying: "inside of your group, a strong subgroup is forming". A survival reaction is to call attention of the remaining group members to destroy this subgroup together before it becomes strong enough. You can avoid this reaction if the subgroup signals weakness, or if it signals loyalty to the currect group leadership; in both cases, the subgroup does not threaten existing order.

Assuming this instinct is real, we can't change it; we can just avoid triggering the reaction. How exactly? One way is to signal harmlessness; but this seems incompatible with our commitment to truth and the spirit of tsuyoku naritai. Other way is to fall below radar by using an obscure technical speach; but this seems incompatible with our goal of raising the sanity waterline (we must be comprehensive to public). Yet other way is to signal loyalty to the regime, such as Singularity Institute publishing in peer-reviewed journals. Even this is difficult, because irrationality is very popular, so by attacking irrationality we inevitable attack many popular things. We should choose our battles wisely. But this is the way I would prefer. Perhaps there is yet another way that I forgot.