Is there a reason to leave WebGL disabled in Safari?
If you're really scared, yes. WebGL allows web developers to code shaders which run unprotected in the GPU. This can cause many security issues because there aren't really any antiviruses to protect against GPU infections.

The risks aren't too great because there are organizations such as Google and Khronos working on making it much safer. These organizations are really quick in creating patches and fixes for issues and flaws.

I'm really not sure about how unsafe WebGL is in Safari, however, because it's based off of Webkit, I'm quite sure it's pretty similar to Chrome.