Ok, that’s completely doable.
Let’s start with the wired bits first. With the router connected to the GPON, do you have a connection to the internet? You will likely need to set up a PPPoE connection on the interface connected to the GPON. When you can ping 8.8.8.8 and google.com from the router, you know that is sorted.
Then use 3 ethernet ports as trunk ports to your three VLAN aware switches, with all VLANs tagged. The thread at http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1 has the sample config to configure this. Make sure you have IPs, IP Pools and DHCP Server Network and DHCP Server for each VLAN configured.
Once you have this, it’s a simple case of setting a data path for each SSID to tag it’s traffic with the appropriate VLAN ID.
The final step is firewalling each VLAN appropriately.