It's a good question and I'm not sure that CarolynUK's answer relates to all circumstances. Certainly, for legacy carriers which sell a good proportion of refundable tickets, check in does act as a quasi check on whether customers are intending to use them. But it's not a perfect check since you can still cancel after check in - and you can still be off-loaded if you don't turn up at the gate on time.
But, at the back of the plane, where most people have non-refundable tickets, a far greater proportion of people actually use the tickets.
I suspect the reality is that no one has taken the step of eliminating it yet. EZ has got close, permitting it up to 30 days prior to the flight. As I always book within that window, it has simply become another step within the booking process and I can see that it could easily be eliminated altogether.