It's so popular because it's elegant, obvious and works very well. Kind of like the format of a book - it's become a default "brochure site" format because it looks professional, it's an obvious layout, responsive and quick and cheap to whack your own graphics in to make it fall in line with a client's CI. And it scales down well for mobile.
I'm not excusing template laziness, but as the web matures it makes sense that layouts will inevitably start becoming more standardized.
And there's nothing wrong with that, per se, provided the designer isn't making out that it's their original creativity at play and trying to charge a fortune for it. For a quick and dirty brochure site that you need to be able to knock out in a couple of hours (that doesn't look like it was designed in MS Word) for not much time and capital outlay, it serves a purpose. For anything more, it should at best be a starting point.