acknowledge his fear. it is real to him. i agree with sitting in there with him, diverting his attention, and then when he is done, reminding him of how well it went. it could be a sensory issue, and perhaps he doesn't like the feel of the cold seat, or even the feel of the cold water when it splashes up when he poops. he could try putting a couple squares of toilet paper in the bowl before he goes to minimize the splash/coldness. and just tell him if it doesn't go down, that's mommy's lovely job to deal with. validate the fear and it will take care of itself. he's old enough to rationalize with. and be glad he's going. some kids won't go at all when they are afraid and worse problems ensue. keep him going!
good luck. the stomach bug is enough to drive any mom to the edge~