It's a ship. People are also under the impression that Wendy and Cartma, or Bebe, or Butters, or whoever, are in love as well- it doesn't mean they are. With Stan and Kyle, it's likely because they're super best friends, and have gotten so close that they're rarely seen without each other. Also, Stan/Kyle butt-pirate stories are good fap material for some creeps and fan girls. And creepy fan girls, mainly the latter.