The overwhelming majority of the enjoyable coffee experiences are caffeinated. While there is good decaf out there it's not the norm, specially in smaller markets.
I think they meant that coffee contains a lot of other compounds than just caffeine, which something like energy drinks or teas will not include. So you can't necessarily extend conclusions from a study on consumption of coffee to effects that other drinks that happen to include caffeine might have.
Edit: this is especially relevant here, as the study found similar effects in decaffeinated coffee drinkers. So the effects they observed, if real, are not related to caffeine.