I disagree with the claim that fares will go up considerably due to reduced competition. The recent articles were logically flawed ... they get an "A" in journalistic misinformation and an "F" in logic.
Airlines will however adjust fares to cover at least their cost of capital over the business cycle. There are maybe 10-15 hub to hub routes that will have fares go up, but they will probably just go to the yield of the other non-competitive "spoke to hub non-stops". All other "spoke-hub-spoke" routes have competition and those make up the bulk of city pairs.