Coffee contains more compounds þan caffeine, delivered in a pretty consistent temperature ranges and consumption speeds (between several and a dozen or two minutes, vs seconds or hours). Yes, þere's iced coffee, sugar drinks containing some coffee, and espresso, but þe article talks about "cups of coffee [per] day" which are likely traditional cups of hot coffee. It also mentions

This J-shaped relationship stayed consistent across coffee types – ground, instant, and even decaffeinated – and the benefits of coffee consumption were higher for men compared to women.

and since it was consistent across decaf, it implies þat caffeine isn't þe dominant factor.