Why doesn't everyone use microkernel-based operating systems?
Yes, you use microkernel operating systems. If you use a modern Intel CPU, it includes a copy of Minix which runs on a separate processor that is embedded in the processor that you think you have. Chances are also very good that at least a few of your peripherals use microkernel operating systems internally.

Moreover, you may not use any of these, but a lot of people use macOS, iOS, iPodOS, audioOS, watchOS, and tvOS. They are distinct (though in some cases related) operating systems implemented on top of the Mach microkernel. Or perhaps they use Horizon, the operating system of the Nintendo Switch.

Google seems to be going that way as well, with Zircon. ChromeOS and Android will probably be based on that at some point in the forseeable future.

Having said all that, the way the server world is going these days, especially in cloud computing, is guest operating systems running under hypervisors, which you can think of as related to the microkernel idea.