The article is spot on. I'm not sure why you are disagreeing. I believe it's the incredibly high pay on the high end of the pilot scale (captains make 250k+ a year) that led to need for this regional shell game that has kept wages so incredibly low (20-30k for a first year FO).
Every major airline manager would love to have the regional flying done in house. They would reap the revenue and profits that would grow their airline and their stock price. Unfortunately, it is the less of two evils to give that flying to regional airlines that keep labor costs low, rather than keeping that flying in house.
Regional FO's should start out at ~50k and Major Captains should end up at ~150k. The higher that top line number goes, the lower that bottom line number will go. The career earnings of a pilot have stayed the same for roughly the last 20 years. It's just where it is distributed that has changed. You can blame the unions for that.