Build a facility with refueling capabilities on the equator, with fuel hauled there if there's no ore locally. Then you build a space station which serves as a fuel, cargo and kerbal depot. Perhaps you can have fuel shuttles from Ike, too.
A kerbal that wishes to travel to a Duna colony would take an interplanetary ship to Duna orbit, then dock with the station (where the interplanetary ship refuels and loads kerbals). The kerbal would then transfer to a shuttle down to the low-port, then take a plane or car to the colony.
Giant interplanetary SSTO's are awesome, but not very practical. Plus, decentralizing colonies like this spreads things out, and makes it look more realistic. It makes colonies feel like colonies, and not like outposts.