I personally didn't get it either.
It's all very good to say that many people have many interpretations, but the artists job is to, at the least, point his audience in a specific direction from which to make that interpretation. Lynch is most definitely a surrealist, but he always provides a context from which to view his work. I didn't find a context from which to view "Mr Fox" so consequently didn't find any meaning in it.
If you got something out of it that's fine for you, but it didn't do anything for me. I didn't even find the imagery especially intriguing for more than one viewing. I've seen plenty of weird experimental pieces; some bored me to tears, others captivated me - different strokes and all that. But the ones that captivated me seemed to capture the rest of the audience as well.
Nothing annoys me more than an artist who complains "you just don't understand"; it is the artists job to communicate with me, not intentionally create something in a secret code and then sneer at me for not being able to break the code. 99% of the time there isn't even a code anyway, it's the supposed artist throwing feces at a blanket and seeing what sticks. These artists are mostly technicians; they know all about and can reproduce the form but have none of the substance of a true artist.