hey there! i fully admit that the game is initially a lil hard to grasp, it's not on you! i just didn't have time to do the tutorialisation that i wanted to.
to get characters to fly, pick the character, select Fly and then click on another island on the spot where you want them to go. they'll head to the nearest plane, fly to that island, and then walk to the spot you clicked. it's the same with the trains. basically just target where you ultimately want characters to go and they will use whatever plane or train they can reach to get there.
i would like to make it clearer how to play but it doesn't feel fair to mess with the game during the jam, so i will hold off on tweaks and improvements until after voting is over. (also i need a break lol)