Earlier versions of ipods were charged using the "firewire" connection pins (though the Dock connector), which is 12 volts. Your Bose SoundDock charges this way.
However, as iPod (internal electronic) design evolved, Apple introduced charging through the USB 5 volt connection and iPods at that time could be charged by either method, both through the Dock Connector plug but on different pins and with a different voltage.
Unfortunately, several manufacturers of various charging/docking devices failed (in my opinion) to heed the obvious, which was that later iPods would not have the firewire connection. Even if Apple didn't make that clear to third party manufacturers (and I don't know if they did or not), it should have been obvious to anyone with technical knowledge that Apple would stop having firewire charging on iPods.
That's precisely what has happened, the iPod touch can only be charged using the 5 volt USB pins. So that's why you see the message *Charging not supported with this accessory* when you place the Touch into your Bose. Later Bose SoundDocks have rectified this and will charge the Touch.
You're not alone, I have a Bose SoundDock, which sure enough, will not charge my iPod Touch, but will charge my iPod Classic. The add-on adaptor in my car, which enables me to connect my iPods to the car stereo via the Dock Connector is the same, it charges the Classic but not the Touch.
Those manufacturers who did see the obvious, introduced USB charging early on in the game. Others were slow off the mark. Klipsch as far as I can tell, actually recalled the RoomGroove so that they could re-work them so they charged using the USB pins. Consequently, my early production Klipsch RoomGroove will not charge my iPod Touch, my later production one will!
If you're really desparate to charge the Touch while it's on the Bose, there is an adaptor by Scosche called the *iPod & iPhone Charging adapter for home docks:*
black is
http://www.scosche.com/consumer-tech/product/1695
white is
http://www.scosche.com/consumer-tech/product/1694
and they both come with the small collar adapotor that fits between an iPod cradle and the Bose base. (What's that all about anyway, why didn't Bose make the hole the correct size?)
There is also a car one -
http://www.scosche.com/consumer-tech/product/1667
Phil