Make is in no way limited to C or C++ projects and there is absolutely nothing wrong in using Make for a JavaScript project.
The only thing that sucks a bit is maintaining the list of inputs and outputs if you have a lot of files.
Well, that and the fact that Makefiles are not generally portable between GNU and BSD Make so if you use both Linux and a BSD you need to install either gmake on BSD or bmake on Linux and then remember to invoke that rather than just make for your project. Of course you could have a bash function that will look and pick GNU make if there is a GNUmakefile in your directory and BSD make if there is a BSDmakefile, but maintaining such things is a hassle as well.
It always comes down to picking the right tool and sometimes Make will be it and sometimes it won’t but whether the output is JavaScript or a PDF (e.g. from LaTeX documents) or JPEGs or whatever has very little to do with it.