There is a tendency where flexible enough parts of OpenGL (i.e. shader scripts) are "misused" to do some stuff not directly related to graphics rendering. An example is skinning on the GPU. However, general animation and kinematics is IMO still done on the CPU.
That isn't misusing OpenGL, that's using properly your GPU. The whole idea of shaders is to give you the programmable ability to do anything you want with it.
Your GPU is by far better at these things than your CPU, and by "these things" I mean applying redundant calculations on big vector-like data sets. Bones (matrices) happen to fit that description.
GPGPU just makes this more obvious (either through OpenCL/CUDA, or compute shaders, if they exist already?).
Updating the animation skeletons, and using IK (which isn't really related to rendering in any way, but rather to physics), though, is usually done on the CPU. There will probably be a time when that, too, wont be true anymore, but we are still not there.