Network Structure
network structure is easy; the two extremes being a hub and spoke system and a point-to-point system. p2p is pretty self-explanatory. You simply connect two airports directly and don't really bother with connecting pax. The hub and spoke system means, you connect everything to your hub (later hubs, plural. This is mostly important in larger regions such as the US, the EU, China, etc, where you might want to operate hubs for regional traffic and transfers, unless you want to connect New York with that farm track somewhere in Alaska directly.
It is possible to operate a p2p service in AS, however, as a beginner, I strongly suggest, you use the hub-and-spoke system. Transfer pax will help you to fill your planes and stablize your load factors in case of external changes like new competition, changing economic index, etc. You can still introduce p2p for very popular routes later on.
for a more thorough explanation of hub and spoke, check wikipedia