Doomsday has adaptive countermeasures, speed that rivals Superman and other speedsters (i.e. Flash) and strength that dwarfs planet busters that outclass the Hulk.
The biggest advantage Doomsday has is it's ability to develop powers, which are reactive to any threat opposed to it. I.e. developing flame breath against Martian Manhunter, energy canceling against Radiant and poisonous claws against Superman. This is coupled by it's ability to regenerate from and adapt to anything that might have killed it.
Doomsday would likely blitz Hulk, overwhelm him and adapt deadly abilities to counter Hulk's gamma based power.
Doomsday would win. Yes The Hulk is a strong being however no matter what he would do to Doomsday it would do nothing to him permanently since Doomsday is a creature that adapts to whatever had previously happened to him and because of his adaptive powers Doomsday would win in a fight against The Hulk.