It has to be cost. There's no question that the reactors can be safely removed and the ship made safe (as least as far as radioactivity is concerned) for visitors. Not only do you have the Nautilus, but EBR-1 (Experimental Breeder Reactor #1) in Idaho has been decommissioned and turned into an historical site with self-guided tours, even inside the reactor room. So 100% decontamination is possible. And EBR-1 was more primitive and probably messier reactor than what drives an aircraft carrier. So, unless there was massive contamination of the ship's structure (which seems unlikely), there's no insurmountable technical issue.
Consequently, I suspect that the reason is the sheer cost of turning an aircraft carrier of that size into a tourist site and then of maintaining it afterwards.
Note that no matter what you choose to do with it -- tourist site, scrap metal, hotel, just letting it rust away, whatever -- you need to pull the reactor and any radioactive elements around it first, so that cost is there regardless. (It's possible that the cheapest way to remove the reactor is to dismantle the ship around it, which would be another reason that preserving the ship was the more expensive option.)