I think it's just the nature of the beast, and an example of a complex problem with a lot of different solutions.

What's broken is the C preprocess/compile/link process. C needs to get a modern module system and ditch the antiquated preprocessor and linker.

I wouldn't claim it's the full story, but IMO part of what's fundamentally broken is the phenomenon of single-language programmers. This leads to the belief that your entire tool chain needs to be written in a single language. So now every language has it's own build tool (or 2, or 3), and god help you if you have a multi-language codebase and need to have a unified build system.

I think it's just down to the popularity of make. People who are starting new projects use make because "everybody's using it, it must be the best!" Then, when make becomes a pain in the butt, they write their own because they've already decided that there's nothing better out there.