Drives connected to Airport do function as TM drives, BUT there have been issues as they are not 'officially' sanctioned. In my experience, I backup my wife's MacBook to a USB 2.0 1TB HDD hooked up to the AEBS and so far over the last month or so, Time Machine has failed to recognize it twice. I can pull data from it, but TM doesn't recognize it as the drive I had been using for my backups, so it refuses to do any additional backing up and it must perform a full backup from scratch again.
To the OP:
Why are you limiting yourself to flash drives and avoiding like the plague one of the best free programs for backing up your data already included with your Mac (Time Machine)?
Buy a 1-2 TB external for around 80-100 bucks, hook it up, run Time Machine and let it do its thing. The first backup will take a few hours, but each additional backup will take a minute or so as it only backs up whatever has changed in the last hour...in some cases that would be nothing (like overnight).
Yes, you can disconnect and it will recover once you reconnect it...although it's likely to run a lot longer to update all the changed files since your last update. And, like someone else has said, if you create and delete a file between updates, those files are lost forever.
I have my external always connected, I rarely see TM even working. It writes some data each hour and then does it again an hour later. I have my TM drive (a MyBook 1.5TB) backing up my internal iMac drive and my external iTunes drive (I have approximately 600GB of iTunes content residing on a 1TB external).
With HDDs as cheap as they are these days, there is no reason to not use Time Machine to its fullest extent. Make sure you buy a drive that is at least 1.5 times the size of your internal. The reason being, that TM allows you to go back in time to pull files you may have deleted months ago or to restore your complete system to a point before you made major changes that caused you grief (as an example). As TM runs, you will build up this history and be able to go back and restore your system with ease.
ASIDE: Buy.com has this 2 TB drive for $89.99 with free shipping.
http://www.buy.com/prod/fantom-g-fo...rive-with-32mb-cache/q/loc/101/219577830.html
All the previous being said, you do need an offsite backup for complete protection (although you certainly have been living with out that thus far). Maybe take your flash drives of your iTunes purchases offsite...or burn them to DVD once a month or so. Or use a cloud service, but be prepared for a HUGE upload when you do your initial backup...it could take a week or more to upload based on your ISP speed and other issues.