After you complete a few Story missions, you gain access to high-tech slideways teleporters that let you travel between the main hubs. These are all well and good, but the Justice League Computer makes things even more convenient!
Press the Map button to call up the Justice League Computer at any time while exploring the hubs. Select the hub that you wish to visit, and you travel straight there, as long as the hub entrance has been built. You can use the Justice League computer from any location in any hub just by pressing the Map button, so be sure to give it a try!