In the absence of the OP, I'm still playing the guessing game. Perhaps they did not have seat assignments? Still, something's amiss if the flights were all on one carrier and the OP was not checked in for both flights together. There's got to be more to the story. I fly several times a month, often making connections, and Delta has always provided boarding passes for both legs. Once you have the boarding pass, with seat assignments, you do not have to check in again at the gate. At least that has not been my experience.
I do agree that it's more prudent for cruise pax to schedule their own flights. All cruise lines, not just RCCL, select the lowest-cost flights, and that often means bad connections (either too long or too short), possibly more than one airline, strange routings, and traveling companions not sitting near each other on the plane. And all do not take responsibility for missed connections. As Dave said, the cruise line will help you get another flight if you are delayed, but they won't do so automatically. Pax still have to ask. And, this is another reason to get travel insurance that covers missed connections.