The OP didn't miss a check-in deadline; they checked in electronically.

The OP was unaware that, like at many small Eagle/US Express stations, the agents leave the check-in desks 45 min to 60 min prior to departure and move to the gate. At some stations, the check-in agents then marshal the planes, operate the jetbridge (where available) and handle the valet bags, before boarding the departing passengers.

Having failed to get to the airport when aa.com and the airport website recommended, the OP was unable to obtain a boarding pass so that they could clear the TSA checkpoint. Not surprisingly, the TSA was also unhelpful.