If you plan on keeping a city, nuking that city basically adds 20-30 worker turns to clearing fallout and pillaged tiles. Oh, and your army moves much slower and it reduces the population by half (and another half after you cap it). That makes capping a size 20 city suddenly a size 5 city that most likely doesn't have usable tiles.
I typically only drop a nuke on a city under three conditions. First, it's a size 40 capital with 150+ defense. Second, it would take significantly longer to use conventional military than to just nuke it, mop up, and move on. Lastly, I'm going to raze it and/or there's a military presence.