Margins are the difference between what it cost, and what you earned. But what I would call "profitability" is your actual return versus capital deployed.
For example, I know a retailer that earns a 1% margin...terrible? No. They turn over their inventory every week (roughly), so they earn that 1% 56x times a year...that is a very profitable business. Similarly, I can earn a 90% margin but if I can only turn my assets over every ten years (some business are like this) then that business isn't very profitable.
Retail provides massive utility. Retail is the link between producers and consumers. Most producers do not have the interest or the ability to sell direct to consumers, it is a totally different (and very expensive) business. And barriers to entry are significant: retail is complex, there are huge fixed costs, and you own the link to consumers (that is why distribution is where all the profit is within most value chains). The internet does make information easier but retailers also do that job, Amazon doesn't but product selection a competitive advantage (most consumers trust retailers more than they trust brands...Amazon's return policy is a prime example, retailers need trust). And there is a difference between providing information and distribution: if that wasn't true Consumer Reports would be the biggest retailer in the world (I actually agree with this a huge amount though, this has never made sense to me...but trust is complex, humans aren't totally logical, and the system we have is pretty good).
I am not clear what your point is. But one, small proportions are fine, Ferrari doesn't sell to everyone and they do okay. Restoration Hardware is a more modern example. Two, your point about those stores is my point about why distribution is profitable. Three, and the point I made earlier is that most of those stores (but not all) have essentially become derivative of each other...and that is why physical retail isn't competitive. Most physical retailers essentially threw up their hands, and decided to compete on price alone which suited online retailers very well (as I said though, this happened when retailers took more control over supply chains and started sourcing directly from factories in China, and this largely started before Amazon existed but accelerated hugely in the 2000s).
I can consolidate these points by mentioning Restoration Hardware again: no-one knew they needed Restoration Hardware before Restoration Hardware existed, their model is ludicrous, it makes no sense...but it is also very successful and gives consumers something they cannot get online. If you asked consumers what they want before cars were invented, they will tell you they want a better horse (btw, Trader Joe's is also the perfect example of this...they did almost everything you shouldn't do in retail, that is how they succeeded).