He is probably scared of falling down the toilet.
Next time, try and put his hands behind him so that he can hold onto the seat to support himself. You must also hold onto him for extra reassurance.
If that fails, sit him the other way round so that he straddles the toilet and he can also hold onto the tank. You can also see if his wee is going into the toilet and not onto the bathroom floor.
I got my son to stand up for a wee by putting a ping pong ball in the loo and getting him to aim for it, it was lots of fun for him and soon he was doing it himself.
I remember being frightened of sitting on the toilet which was made worse because at times my wee used to end up on the floor and my mother used to shout at me and then smack me for being a bad boy.
I think my mother was trying to bring me up as a girl because I was the only male in the house and my two sisters were older than me.
It was only when I started school that I found out boys stood up to wee.
I would stand him up and let him aim at a ping pong ball like another respondent suggests.
Have you tried a training seat. My son loved it, its just big enough for their little bottoms and no way they can fall in. I got it for him as a present for doing so well with the potty, he couldn't wait to try it. I even put a stool in the toilet and kept the training seat there permenantly and he started doing it himself. I wasn't even allowed in the toilet when he went!