WebGL is a newer technology that is a port of OpenGL to the web. It is generally slower however.
When this option is disabled, it uses your browser’s native canvas API. Not all browsers have the canvas API, however. This is why WebGL exists, to enable support for older browsers.
Just depends on your computer, usually Canvas is faster on older or smaller devices like mobile or tablets and even some older pcs, but on newer devices like iPhones iPads or on computers with a graphic card you will get better fps with WebGL on. Most people on decent hardware won’t tell a difference though.