Might depend on which Superman you are referring to. Silver Age Superman would probably have no problem, since he was "nigh invulnerable." He got weaker with the Byrne reboot, and since then, I have no clue how powerful or weak he is. Energy form Superman would probably lose. I know Supes was pretty weak on the cartoons, where he would get tossed around by robots and whatnot pretty easily. Hulk had different incarnations, too. But yeah, if Superman kept flying away, then it seems like Hulk couldn't stop him easily. But could Superman really beat Hulk with heat vision?? Nah.
And Supes could throw him into space and let him suffocate. Or toss him into the sun. Except for one problem--Superman has a moral code. He wouldn't kill Hulk unless he absolutely had to as a last resort. So could he incapacitate Hulk without killing him, without resorting to the help of Batman or one of his other buddies? Not sure. Plus, Supes always seems more concerned with innocent bystanders than Hulk, so that's an extra advantage Hulk has, because Supes is always getting distracted with protecting innocent people or animals or whatever.
I'm not so sure Hulk couldn't win a war of attrition where Supes eventually got tired of flying, Hulk caught him off-guard, and that's all it took. Hulk starts beating the tar out of Supes and doesn't let up until he's beat to a pulp.
If Doomsday could do it, so can Hulk.