I don't see any downside to automatic check-in or online check-in and plenty of upside. For an elite, it puts you in the upgrade queue earlier than if you wait to check-in at the airport. This can very well be the difference between getting upgraded and sitting in the back. In addition, it gives you more latitude if you are running late. Instead of being subject to the potentially harsh consequences of not arriving at the airport and reaching the front of the check-in line at least 30/60 minutes before the departure time, a passenger is only too late if not in the boarding area and ready to board 15 minutes before departure because it is not until then that CO knows that said passenger is either tardy or not going to show at all.

Regardless of whether I have access to a printer or not, I always use online check-in (except when a glitch prevents me from doing so), and I appreciate the automatic check-in feature, except as it disadvantages me when I am beat to the punch by other same-status, same-fare-class elites when my outbound segment, requiring manual check-in, is their automatic check-in-enabled return. But since that tends to even out . . .

If online check-in and automatic online check-in don't sit well with you for some reason, ignore it and go about your business as if it didn't even exist. Stand in the line at the airport, collect your boarding pass from a kiosk or agent, and proceed through security and onto the gate.