The administrator has the option of making any port access, or making it a trunk. The access port can pass any vlan, and the trunk can pass a number of different VLANs. It does not just have to be VLAN 1; that is just an example. When you define a WLAN, and the traffic is tunneled back to the controller, the user traffic can be placed on any VLAN that is on an access or trunk port connected to the controller.
For example, the controller can have a trunk connected to a router that is passing VLANs 10, 20 and 30. I can have 3 WLAN defined - an Employee WLAN on VLAN 10, a Device WLAN on VLAN 20 and a Guest WLAN on VLAN 30. Any access point that is deployed can tunnel the traffic back to the controller and the controller will place the user traffic on VLAN 10, 20 or 30, depending on the WLAN that the user is connected to (Employee, Device or Guest). It does not matter what VLAN the access point is on, as long as it is routable to the ip address of the controller and can send traffic to it; Everything is sorted out when it gets to the controller.
I hope that helps.