The most obvious answer is that not everyone checks luggage. I go to the counter maybe 10% of the time that I fly, as I very rarely have bags to check.
Even if you are checking bags, the online check-in system allows much of the process to be completed before you arrive to drop off your bags. Depending on the airline and the flight, that could include everything from picking the seats you want, entering details of passports and visas that may be required, right up to paying for the baggage that you will be checking in advance.
For many airlines, all that is required during bag drop is to scan the pre-printed boarding pass, print off the baggage tags and attach them - far less than would be required if the passenger had not checked in already.
If nothing else, online check-in is a feature that is now pretty much considered mandatory by passengers. Personally if an airline didn't offer online check-in, I would hesitate before booking, and potentially book with another airline as a result.
As far as return on investment, the simple fact is that almost every airline in the world now days has online check-in. If it was not a net benefit to the airline - either from a cost perspective or from a potential lost business due to customer satisfaction - then this would not be the case.