It's far more expensive than just plain flat glass and it's not really necessary in most cases. E.g. for scanning film, most flatbed scanners (if they support film scanning in the first place) come with film holders that raise the film a bit above the glass so it's no physical contact. Some film holders do use (plain) glass (e.g. later Epson flatbed scanners) and those are also know to cause similar issues. What helps in most cases is that if you scan film (not Instax) with the emulsion side on the glass, there are usually no Newton rings because the emulsion side on many films (esp B&W) is a little rough. This is not true for films like Kodak TMAX as well as Kodak color films, which also readily make Newton rings when in direct contact with glass.
Short answer is still: because of the cost.
That’s actually really interesting. Some time ago I spent a lot of time researching scanners I even asked about them here on the forum but eventually I realized that, for the quality I wanted, it would probably be both better and cheaper to simply take my photos to a professional lab for development and scanning.
I also considered using a digital camera to digitize my Instax photos through camera scanning, but I tend to avoid borrowing expensive gear like that from other people.
At one point I thought about just using my iPhone camera, but after watching a few videos online, I noticed that reflections of the person taking the photo often appeared on the glossy Instax surface. Honestly, I thought it looked kind of awkward and unprofessional. Not that I’m a professional myself far from it, actually I just really like things to look as clean and “perfect” as possible, you know?
So if I can’t find a lab nearby that can properly scan them, I guess I’ll end up going with a scanner after all. But I definitely don’t want to invest in one until I’m completely sure the scans won’t end up with those awful Newton rings.
I think it's worth noting that there are Instax cameras (and Instax backs for medium and large format cameras) that will give you more control over your exposure. For example, I have a MiNT SF-670 that is a rangefinder with full manual and aperture priority exposure control. Some of Fuji's current cameras give you a bit more control than the Instax 100 (but not full manual shutter/aperture settings). The Instax 100 is interesting as it was the first Instax Wide camera, though.
For scanning, I 3D printed a frame that holds the photo just above the scanner glass so that there's an air gap between the surface of the photo and the scanner glass. I also sometimes use my camera scanning setup (mostly used for 35mm film) to scan instant photos.
I watched a few videos of people scanning Instax photos using scanners like the Canon LiDE 300 and the Epson Perfection V39, and honestly I couldn’t really notice any Newton rings in the results they were getting.
Of course, to achieve something on a higher level like your scans, I imagine I’d probably need a CCD scanner instead, which is also something I’ve been considering as an option.