From my experience of explaining APIs, most people don't understand the distinction between the web and software, let alone the difference between a web-based API and a software one. If a user knew what WebGL actually is, I would guess that they already know what an API is.
Web services, of course, tend to have web-based APIs. But that's a subset of all APIs.
Since this article seems aimed at beginners, I think it's an important distinction to note. You would not want beginners to think that APIs are always web-based because then they'll be confused by things like WebGL, which is also an API but does not involve web requests or AJAX.