The Enterprise is a “ship of exploration” in a way that’s not possible today. You’re misunderstanding them. They’re like a explorer’s ship in the “Age of Exploration”, Captain Cook or Magellan or Christopher Columbus. Although their mission is slightly different: diplomacy vs. claiming territory.
All those ships were fast and had weapons too. Diplomacy requires weapons. Starfleet is clearly not a military. Even civilian ships today have “captains”, “first officers”, etc. Cruise ships have them. Even pirate ships had them. Rank and hierarchy is not exclusive to the Navy / military.