IMO, the main issue with Boost.Build is just lack of documentation. There's a reference manual, but it leaves out a lot of stuff (like auto-configuration) that's pretty much necessary to use it. The home page also lacks any kind of convincing examples.

Also, a lot of companies looking into C++ build systems want blazing-fast speed. Unfortunately, b2 isn't necessarily the fastest build system (although CMake's make generator isn't, either).

And the error messages. Oh lord, the error messages.

TL;DR: after a brief visit to the home page, there's no obvious reason to use it, the reference manual doesn't have anything to put everything it mentions together, and the only experiment with b2 the user ever does results in a 10-second wait before an error traceback referring to obscure terminology that they don't understand.