Having worked at (and briefly managed) a local computer store, then a big box store, it's a brutal business. In the small store we made all our money on service: selling recycled commodity boxes was a way to get traffic through the door, so you could fix them later. A few high-end builds were the highlight of my year, but they were few and far between. We considered offering Linux, but:
- It used to be that most technical people ( and some non-technical) would buy desktops. You can sidestep the Windows tax and attendant issues by building a desktop (from parts you know work well with Linux), and maybe hit a competitive price in the high end. Now that desktops are a tiny sliver of the market, these stores are enslaved by OEMs, reboxing existing laptop designs.
- Starting from the same wholesale price, Linux resellers 'add value' by installing Linux. But this value-add isn't really apparent to a large enough audience - there isn't enough public awareness, and people aren't willing to pay a premium. Especially if they're competent enough to install Linux themselves. In my experience people expect ANY OS to be free; when we used to try and sell Win XP as an upgrade (over 2K), people were aghast that the software cost money.
- People want free support if you sell them on Linux. If they nuke the system, you either scare them off with your hourly service rate, or you eat the cost of the labour and go broke.
- So the vendor either charges a higher sticker price and doesn't sell many, or eats the labour cost for developing Linux support, fixing and reboxing laptops and tries to make up the tiny (or even negative) gross margin on volume.
When I moved to a bigger chain store, they subsidized the low-margin laptop market by aggressively pushing house-brand accessories: cables, cases, blank media, printer ink. These small stores are typically much less aggressive about selling high-margin commodities along with a system (it's harder to do with less capital, space and by mail).
So it isn't a problem of freedom and choice. It isn't a problem of Microsoft crushing little independents (not consciously). The computer business is very hard to do well at small scale, and you should expect that on a medium time-scale most will die. This is only exacerbated by the rush to laptops, then tablets and smartphones, where it's impossible to differentiate.