Just played and captured my first flag..
First off when you do finally make it in to the base fly low you have to touch the flag not the light itself then high tail it out off there back to your base. Now if you think you're going to get shot down hit the flag button at the and drop it before you go down or it returns back to the enemy base and you start all over again.
When you do finally make it back, fly low just like you did when you picked up the enemy flag and it's over.
You need to have both flags aboard your plane back at your base.
Hope that helps, I didn't notice how many points it gives for actually capturing the flag though.
It's kinda like dogfighting with a twist..

A little strategy and team chat is a must for this one.
Have fun and good luck..