Well, for me, beating a dead horse is such a common phrase that I often use it without considering a less figurative interpretation of it. When I actually see a horse, dead, being flogged and abused its not inherantly funny. But the inference I make between the saying I use and the imagery is pretty funny.
Another funny thing about "beating a dead horse" specifically is I think that the imagery involved doesn't necessarily involve the phrase's origin. I would think that the line "beating a dead horse" refers to a horse that has been ridden and died, yet its rider continues to prod its lifeless body trying to squeeze a few more miles out of it.