I know some kid think of the bpoop as part of their body and don't like to see it go down the toilet, and also some have trouble "pushing" it out in the sitting position on the toilet, withnothing to brace their feet against, when they are used to squatting, and using those leg muscles to help push it out.
So my 2 suggestions are this - see if you can find a kids book about digestion and poop, or just talk about it yourself, and explain to him that poop is the "garbage" your body leaves behind after it uses up all the good stuff in your food, and that the toilet is the "garbage can" for poop. Then also, make sure there is a way for him to use his legs to push when pooping on the toilet. If it is close to a wall, have him sit sideways and push his feet on the wall, or if you can find a step stool tall enough, make sure his feet touch while sitting, and let him squat over the toilet, with feet on the stool, hands on each side of the seat to poop - or if all else fails, "help" him - by using your hands to push on his feet as he is sitting, so he has something to push against.
These books might help some - check your local library too:
http://www.amazon.com/Chew-Poop-Pee-Express-Digestive/dp/...
http://www.amazon.com/Wheres-Poop-Julie-Markes/dp/0060530...
http://www.amazon.com/Zoo-Poo-Richard-Lyon-Morgan/dp/0099...
http://www.amazon.com/Journey-Mister-viaje-Spanish-Englis...
http://www.amazon.com/Free-Poop-Kiki-Kukaluka/dp/06153253...