Because their customers are breaking the law? I agree that there's an issue with how to handle jurisdiction, but you can hardly ignore a court and then get mad when they take action against you.
Just because someone is setting up blocking does not mean that a law has been broken.
Blocking is often used as an easy alternative to prove in courts that laws has been broken.
For example considering the list mentioned in the article (and I do not know which ones affected cloudflare):
http://netzsperre.liwest.at/
Why should a US company censor a Russian website (rt.com) because it is on a Austrian list because of a EU regulation? Austrian citizens reading rt.com are not breaking the law.
And I better add, that I am not claiming that the content of those sites are trustworthy, but I do feel insulted that they do not trust me to read if I want to.
Because their customers are breaking the law? I agree that there's an issue with how to handle jurisdiction, but you can hardly ignore a court and then get mad when they take action against you.