Well its just that.. right now you can only assign a VLAN to a physical interface on the Mikrotik.. Sometimes you have hosts that connect through multiple interfaces that you want to group logically. Well with port based VLANs you can not do that, everything connected to that physical interface is part of that VLAN..
When you group VLANs based on a devices MAC address you can have multiple logical networks that span multiple interfaces.. for example you could put all your CPE/microPOP's on one VLAN grouping them by their MAC addresses and your customer devices on another VLAN...
You can also group VLANs based on protocol, or IP address. Our managed L2 switch does this, but it'd be nice to have in the Mikrotik as well.
If I didn't explain that well enough you can read more on VLANs here:
http://en.wikipedia.org/wiki/VLAN