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I believe they meant "why people are so up in arms about the developer being so strict about enforcing their trademark," not "why are people upset that the port author is being deceptive."

Ahh, that reframe makes a lot more sense

The people were up in arms against the Notepad++ author doing something about the deception.

Which was why they felt they had to write this post. Read the article.

The difference is intent. It will deceive people whether or not the author's intent is deception.

People are upset about the deceptive misuse of the trademark. Rightfully so, it’s deceptive and misleading, legal issues aside.