Are there other times when he doesn't like laying down?
Is the changing table cold or a fabric that may be uncomfortable to him? Have you tried cleaning him up with just a warm water, moistened diaper - if you use wipes, maybe it's the wipes irritating his skin or they are too cold. If you really like wipes, try holding them between your hands to warm them up before putting them on his skin.
Does he like being diaper-less at other times? Maybe let him be "naked" for a few minutes after you clean him up?
Does he stand yet if he has something to hold onto? It's not as easy but still possible to change diapers while they are standing. Do you get the same reaction with him just standing on the floor (hardwood or tile, of course *wink*).
Another thought is, did he ever get hurt or frightened while on the changing table - poked with a pin if you use pins with cloth diapers (wraps are great!) or pinched with the tabs if he had disposable diapers, almost roll off, does he just not like being at the height of the table.
What if you change him on the floor? - same reaction? What if you change him away from home? Or is it only the changing table?
Also, it may just be a phase (which too will pass *grin*). Seems to me one of my grandkids just didn't like being restricted from moving around - can't be bothered having to stop... having too much fun learning and exploring.
Good luck - keep trying different places and ways of changing the diapers ... you may find the clue or he'll just decide, "oh OK Mommy". ~M.