Is there any way I can keep Pro Tools 6.1.2 from putting a "Digidesign Databases" folder on my iPod every time I launch Pro Tools with my iPod mounted?
Unfortunately not. This has been discussed a bunch of times (search for "DigiDesign Databases"). The only solution is not to have Pro Tools running when your iPod is mounted.
Just another example of Digi's sloppy, intrusive, disrespectful and maddeningly frustrating way of doing things. No consideration for their customers or their customers' machines.