One obvious difference I can see at a glance is that Maker.js doesn't support 3D models, while FluidCAD does. I assume Maker.js is a lower level library aimed at interfacing directly with CNC machines, while FluidCAD is focused on 3D design.

Maker.js is supposed to also support openjscad (or whatever they're call it these days, the JavaScript enabled version of OpenSCAD).