I think it's because PC ended up being the shortened form of the IBM PC, which has (pretty much) always been a Wintel box. Prior to that, personal computers (without capitals) were generally known as microcomputers, home computers, workstations etc. I think, I'm Old and my memory's not what it was, and it was never much!
You are right, it's definitely caused by the very long domination of Windows as the most used PC OS. Things are changing now however, so this association (PC = Windows) starts looking more and more weird. The most inconsistent case is when developers write: "the game will be released on PC, Mac and Linux". This mixing up the hardware platform with the OS right in one sentence really catches the eye and I think they should know better.
It doesn't help that Apple helped enforce that a while back, with their "Mac vs PC" ads. I agree that it should be Win/Mac/Linux, but it's seemingly ingrained in people.
That may be made some sense in the past, when Apple was contrasting x86 based PC with their PowerPC Macintosh. However they since long switched to x86 as well, essentially making Macintosh equal to PC hardware wise with the only differentiating factor being the operating system (OS X). This contrast however was stuck because other alternatives like Linux / *BSD were still quite below the radar.
With wider Linux usage that we see now (including in gaming) this will start to improve. But reminding developers about using proper terms wouldn't hurt
