The court has stated if they want to extend their authority to the level they are enacting then congress must pass laws to expressly denote that intention.
States have rights in the original law. They are exercising this right and the court has agreed with them.
I think the last sentence in the original article sum's up why people are truly upset. Remember the court didn't say the EPA can't do these things in the future just that Congress would have to give it the authority.
From the original article:
"It's now clear this court will turn a sceptical eye to agency attempts to cite vague or broad laws to enact any sort of major regulatory changes. That's a significant development, given how difficult it has been for Congress to pass substantive new legislation in recent years. The time when presidents could find unilateral "work-arounds" in existing law may be coming to an end."
[0] https://www.govinfo.gov/content/pkg/USCODE-2013-title42/html...