You have to understand the whole "protecting their copyright" thing I think.
Obviously Mr. Homebrewer isn't going to put a dent into their pockets. But if they allow him to violate their copyright, they're *screwed* when someone else comes along, creates their own 'fan version' of Chrono Trigger and has the backing of, say, Atlus.
Atlus argues that Squenix didn't protect their copyright in the case of Mr. Homebrewer, so Squenix has therefore given up that right according to copyright law. Atlus wins, and goes on to make a *fortune* at Squenix's expense.
I can see someone then arguing "what would the odds be that an Atlus would *do* that though" and I'd have to reply "why would a Squenix *ever* put themselves at risk, even if it's minimal, with their IP?" Your IP is what makes your company unique - give that up and you're screwed.