Great idea, I think it could be really useful.
I'd like it even more if you decrease the focus on the giant map and instead have a little form like
+--------------------------------+
| Leaving from: ______________ |
| |
| Going to: ______________ |
| |
| [Show me] |
+--------------------------------+
Show me a mini map for my end points and let the rest of the screen show what flights I can take. Maybe with some controls to let me filter on things like "what car rental my company uses", "time on train from airport to city center".
Let me pick specific airports... but don't force me to.