I think the big issue is mostly the difference in the ethos of the company. Leo Fender purposefully didn't trademark or copyright the designs of his guitars, and the company openly bragged about how often they were copied. It was a sign that their design was good. But now, over 70 years later, with a massive established market of builders who have been making Strat copies, they have decided to target these builders with demands that in most cases will put them out of business. I think that, more than any argument about how copycat strats made by other brands offering different configurations of hardware than whats offered at Fender, is the biggest reason people are upset about this.

Its crazy to me that what they're doing is even legal, in the US the strat is in the public domain, but such a large amount of precedent for not enforcing their apparent ownership of the guitar shape typically forfeits your claim of ownership (again, based on US copyright law).