One aspect of this debate that seems to have been overlooked is status, earned through long term loyalty to the airline. I fly from Seattle to Denver a lot. I have a choice of four airlines. Alaska Airlines gets the bulk of my business and one of their ways of thanking me for consistently directing my business (money) to them is rewarding me with early boarding once I've earned a certain number of miles flying with them.

Assuming you agree with the awarding of perks (such as early zone boarding) associated with having directed a lot of your business (money) towards a specific airline:

Should that perk be denied or overlooked just because you chose to purchase a less expensive ticket on a given flight?

You're saying boarding priority should be about the price of your ticket for any given flight but you fail to consider that the priority boarding person ahead of you traveling on that $99.00 fare has earned the right to that early boarding by having spent (or directed to be spent) thousands of dollars worth of travel towards that airline.