Indy, shareware and homebrew games don't represent the video game industry. For example there's an indy game about beating up Anita Sarkeesian. And there's rape simulators, school shooting games etc. You could never publish a commercial game like that. You can make an indy game out of anything since there isn't a budget on the line, nor are there any publishers to censor the content and dictate what the game should be like.
It's fair to make generalizations of the video game industry's unwillingness to make/publish certain kind of games these days because it's a fact. Some legendary video game designers are asking money in kickstarter these days because publishers refuse to publish oldschool RPGs, adventure games, space sims etc because it's "too risky, not enough people would buy it". And with many of these genres, it's basically impossible to do a proper game if you're an indie developer, so it's a fact that certain type of games that were produced in the 1990s and early 2000s aren't being made anymore, commercial nor indy. You can't make a large oldschool RPG with a 0 budget and 2-3 guys. Or you can, but it will take an eternity to finish. Hence we don't see any of those certain types of games being made anymore these days, they are too risky for publishers and require too much resources and people to be made by indy developers.
It's stupid to ignore indy games as a whole, but it's a fact the indy game scene isn't a part of the video game industry and the image of gaming. 2D platformers, shmups and beat em ups are a good example. During the 1980s and 1990s they were prominent, a part of both media and mental image of what video games are, because there were tons of commercial games of those genres being developed for consoles, home computers and arcades, so they were visible part of the video game industry. Nowadays games like that are still being developed by indie developers, but they aren't visible in TV commercials, gaming magazines etc as commercial game developers don't make games like that. When you're trying to find games to buy for your Xbox or Playstation, there aren't any like that available. Although thanks to Xbox Live Arcade and PSN that situation is starting to change, so what I just said was more true during the PS2/Xbox/Gamecube era (I'm sure some one will try to correct me on this and mention Viewtiful Joe

).
When we think of different eras in gaming, our mental image of them is defined by the commercial games that were released during those times. Here on these forums we spend a great deal of time talking about Genesis and Super Nintendo games but yet we don't talk about early 1990s indy games at all really. Our mental image of the early 1990s (in video games) is shaped by the commercial console, computer and arcade games of that time.