Simply put, people using C++ on the web, are doing so because they are unwilling to learn another language.
This is certainly true, it allows them to get productive quickly with whatever languages they already know.
For me, it is a portability issue. I know with C++ I can write my game once and know it can be compiled on every platform under the sun with minimal rewrite of the core boilerplate (boring) bits. I cant seem to find a single javascript platform that works on more than one or two platforms (including 3D) whilst still offering me enough flexibility to also use native libraries when required.
Plus the javascript emitted by Emscripten has the LLVM optimizations as a bonus so runs much faster than what I could manually write.