If you measure by "number of users of the resulting binaries", Ninja is primarily used as a backend for Chrome's bespoke build system. But by number of projects, cmake is likely dominant.

(And yes, part of the reason Ninja succeeded is because it ties the hands of the person generating the files. Make gives people enough rope to hang themselves and they frequently do. From the manual: "To restate, Ninja is faster than other build systems because it is painfully simple. You must tell Ninja exactly what to do when you create your project’s .ninja files.")