I'm not all for closing hatcheries. I do, however, feel that most of our hatcheries aren't giving us a good return for our dollar. I also accept that there are negative impacts from our hatcheries. Impacts such as...
1. Hatchery fish do poorly when spawning in the wild. Hatchery x native crosses result in fewer natives returning.
2. Hatchery fish fuel many fisheries, commercial and sport, that result in the death of many wild fish (by-catch).
3. Young hatchery fish compete with young wild fish. I don't know to what degree, but it happens.
4. High populations of hatchery fish (say outmigrating smolt) can create high populations of predators, which then also prey on the wild fish that are mingled in. For example, Skagit merganser populations may be inflated because of all the hatchery raised steelhead, coho, and chinook smolt in the river at certain times of year.

Other issues like water quality downstream of hatcheries, and possibility of disease transmission are out there, but I don't know much about them.