I had the liner out of the trunk over the weekend and I noticed that are vents (with soft rubber louvers/flaps) on either side of the trunk. Any ideas what they are for? Thanks.

They allow air to exit the car when you shut a door / trunk. Makes it easier to shut the doors / trunk.

They are the other half of your heater vent system - you can't have an outside inlet, and a three speed fan, without somewhere for the air to get out.

S

Ah...that makes sense.

I thought the other half of my heater system was all the heat that comes through the center console. :)

That's the 1st half. When you turn on the heater, a vent sucks air from the center console and pushed it through the vents ;)