There's a way to do it, but it can be predatory.
a) Dominate a route. Send about 10 planes through that city. Make the second leg of your flight from that city to whatever city you want. First city becomes your second hub. (This is the predatory way.)
b) Run second leg of the flight to a hub or focus city. Create a flight to somewhere, make the second leg to your second hub city. I did this with my airline in JA#1. I hubbed in Glasgow, with a second hub in Prestwick. So I made my flights outbound to somewhere, second leg to Prestwick, and return. This way is less predatory, but there will still be competition.
There ya go. Not modeled in the game, but people smarter than me have figured it out.