The difference is popular conception. Laws aren’t set based on science. They’re set based on what enough people believe. People believe energy drinks are worse and thus they get regulated whether or not it’s true.

Advertising, audience, and stereotypes play a part in this too. Coffee is stereotypically consumed by older people, whereas energy drinks are often younger people (who older people find annoying). Coffee also has a much greater social acceptance that would make it controversial to regulate. End result is that it’s popular to limit energy drinks but unpopular to point out that coffee has far more caffeine.