A rather late reply.... It depends on the dock. Some work just fine with Rockbox and some work partially, and some don't allow any control of the iPod. For example, the second version of the Apple Universal Dock, A1256, works perfectly, but the third version, A1371, doesn't control the iPod at all under Rockbox. There is some information here -
https://www.rockbox.org/wiki/IpodAccessoriesI also have a on-Apple dock, I can't remember which one, which will stop/pause/play OK, but FF and RW will only do those functions within a track, not skip tracks.