Zero economic profit holds only in equilibrium and there are no markets where equilibrium ever holds for long because the global and local economy is constantly in flux and entrepreneurs are constantly trying to find new ways to solve old problems cheaper or new markets or ways to solve a problem when one of the inputs suddenly dectupled in price.
The system is working well if 90% of revenue is profit at pip squeak levels, yes. If Microsoft could manage 90% profit margins on billions of dollars of working capital that would be concerning. Individuals or small companies finding tiny market imperfections and becoming wildly rich exploiting them is the system working, incentivising people to produce value.
Schumpeter: Entrepreneurs make new things and that’s great. Outside capitalism those people turn that energy into taking more of the pie, as warlords or tax farmers. Capitalism is better.
McCloskey: Capitalism is good because it inculcates patience, diligence and tolerance in people.
[1] http://libgen.is/book/index.phpmd5=21EE8F203D5C3F9530D55985B...
[2] https://press.uchicago.edu/ucp/books/book/chicago/B/bo375063...