OpenGL support has been in Java for 6 or 7 years. WebGL has been in browsers less than 12 months and Java isn't even twice as fast?
(I'm a long time Java programmer, but I think JavaFX is the most stupid thing I've ever seen)
So while you may get better perf in a micro benchmark like this, with decent graphics hardware you should be able to add 2000x the content (vertices, fragments, textures, etc) to the WebGL app with only a little increase in GPU (and CPU) load.
Comparing anything to WebGL is silly as WebGL may run on different hardware and software, ranging from a mid-spec smartphone to a hot gaming PC that has liquid cooling and it's own nuclear power plant for power supply.