Yes and no, if you have a look at most linux desktops, they don't use full 3D rendering unless you enable it specifically - 3D rendering is heavy and power hungry.
What I believe will happen with WebGL is that it will be used for niche applications (things that needs to be in 3D) as well as replacing things that could only be done in Adobe Flash in the past while the rest of the web will continue to use simple animations that are not WebGL.