There are multiple instances of planets that have multiple settlements, towns, or cities. Tatooine has been mentioned alread. Naboo has Theed, Otoh Gunga, and the Lake Country.
However, the true question here is why characters choose to leave the planet when on the run instead of attempting to hide out in a settlement/town on the same planet. The fact is, they do both. The Gungans abandoned Otoh Gunga and go to The Sacred Place when under attack by the Trade Federation.
That said, when faced with a threat that can track you wherever you go in 'normal' space, Hyperspace is the only option. This is why most characters will leave a planet and/or entire system in order to escape a foe.