If you run a search in the accessories forum, you'll find the various solutions people have come up with--ranging from "don't use the bumper" to enlarging the dock connector slot with a Dremel tool to trimming down the plastic housing on your cables.
Eventually, a dock extender will be available that fits the bumper. I know SendStation is working on one already. But yeah, Apple screwed us majorly on this one in the meantime.
Edit--glad to see you made it work! I've been lucky, all my cables are USB and easily replaced, but I've been tempted to cut mine to fit my speaker docks.