There was a time when queues at post offices and banks etc were counter-specific. Eventually it was widely recognised that a penning system (a Single-Line queue), or ticketing systems and such like, feeding all counters offered efficiencies.
Check in counters at airports are sometimes run with penning systems or the equivalent, but only ever in my experience by a specific airline or that airline plus some affiliates. That often leaves long periods on some days where scores of counters are unmanned and with nobody waiting, while other areas may be heavily crowded with people waiting to check-in at a handful of counters. It is unlikely that all the counters would be in use at any one time given the number of passengers in a short time interval that would imply and the limitations of other facilities at the airport (Security, ground-handling tugs etc).
Edit This last is my misconception. See @Tom’s answer – at peak times all counters are used. (Subject to @SpaceDog's proviso re new airports.)
According to some “The airline industry, in its history, has never made money.” and though that is disputed, the industry is clearly very sensitive to costs eg. With that in mind, many airlines subcontract ground handling to airport owners, handling agents or even other airlines. More than 50% of the ground handling is outsourced where ground-handling includes check-in counter services for departing PAX.
Except perhaps for El Al Israel Airlines, the procedures for checking-in at any one airport (eg whether the exit fee, if any, has been paid) are similar for all international flights from that airport. The available technology (eg baggage handling) is the same and apparently staff may switch between counters (almost?) regardless of airline. So check-in services are a commodity with little differentiation other than the badge on the clerk or the banner behind the counter.
It is only curiosity (or perhaps something to do with?) but why are we wasting valuable real-estate by leaving it idle for quite long periods – and consequently causing passengers to queue longer than otherwise and presumably, somewhere down the line, charging them for the ‘privilege’?
I’m guessing there is some technical reason, rather than merely a failure to agree commercial terms for a centralised service. Staff training is perhaps the most likely but does not convince me at present. I appreciate that shorter queues might not reduce the time between my arrival at the airport and my boarding my aircraft, but if it must be spent I'd rather do so in a Lounge.