How is that really inventing anything? They're either following instructions to use a product, or doing something completely obvious.

Maybe I'm misunderstanding the intent of patents, but I would've thought they protected the interests of the inventor against competition by other inventors rather than users of an invented product?

I don't know the specifics of this man's legal claims, but the article makes his stance pretty clear: the combination of scanning, emailing, LAN and one-button operation is the thing that is patented. The point is not that the user is inventing something, it's that somebody else has invented this combination, and the user must now (again, according to this man) pay a license fee to use this specific invention.

"or doing something completely obvious."

This is also discussed in the article. Many things that many people (especially engineers) would consider 'obvious' or 'simple' really aren't under patent law (again, this mans claims), and in some cases, things that are 'obvious' now weren't when the invention was done. Which, to some degree, is true.

"Maybe I'm misunderstanding the intent of patents, but I would've thought they protected the interests of the inventor against competition by other inventors rather than users of an invented product?"

No, the point is to protect inventors by giving them a way to control under what circumstances (i.e., in most cases, after how much money has been paid) their invention can be used. Patents aren't about preventing other from inventing the same thing again, it's about having a monopoly on using/commercializing the invention.

Inventing ... Is not the issue. There are several ways to infringe a patent, and one of them is "practicing" it. This is likely the legal theory for finding infringement here.