It seems that it's really pointless in many instances, especially abroad.
A couple of weeks ago, I checked in online for my JetBlue flight out of SJO the day before. I printed my boarding pass and only had a carry-on. I know you have to pay the exit tax so you have to go to the check in line and see the person at the little stand they have set up as you enter the check in line. So I hand them my passport, boarding pass, and exit tax, and he looks at it and tells me to get in line (shorter line). I asked what for since I have a boarding pass, paid my tax, and I have no luggage to check in. Just like everywhere else in Costa Rica, you get no sensible reason just are told that's the rules. So after a few minutes, I get to the counter and hand the guy my paperwork and he starts to look it over. Then he turns to his colleague and asks what time it is. I'm thinking WTF is he worried about, it's 90 minutes before the flight. he finished "checking me in", even though I thought I was already checked in, and then I asked him about the time thing.
He says that I almost didn't make it. It seems that whether or not you check in online, you still need to be there 2 hours before the flight. What is the point of doing the online check in?
It's not only in Costa Rica, same shit happened to me in Dominican Republic (POP), and coincidentally with JB, maybe it's an airline thing. I think Taca never made me go check in to the counter, they took the exit tax form and sent me to the gate.