"How is the general "occasionally" traveling public expected to know the difference between published and non published fares when going to the website and buying what the airline itself offers? Doesn't that make it a published fare if they publish it on their website? Where is this clearly and simply explained?"

I think you mean "restricted" and "unrestricted" fares. Unpublished fares are a different matter and it is generally accepted that these will not earn FF credit. These are occasionally available on airline web sites, but are not the same as the vast majority of fares offered on these sites. Unpublished fares are also provided to the travel industry, and through consolidators [with varying accrual rules]. Or Priceline type fares.

The changes being announced by most carriers related to discounted tickets which are the usual type sold on airline websites and by TAs and internet services like expedia and travelocity. Because they require Saturday overnight and/or have other restrcitions, these are known as non-refundable, or restricted fares. Refundable or unrestricted fares, a basically full Y, C/J or F/P/R which have minor restrictions but otherwise are fully flexible, often accepted [endorseable] by other competing carriers.

As for the conspiracy, I don't really believe in them. I just see this as a logical step towards clearly defining what each fare class now provides, and what additional charges will be to add levels of flexibility to the base ticket price. This is differentiating the product beyond the notion that an airline seat is just an airline seat. Full service carriers want us to now realize that beyond the reserved seat on a given flight, we will have to pay for each additional item: standby, change, upgrade, etc.