This depends on your dock. If you have the universal dock which uses dock adapters, I find that if I take the dock adapter for the Classic iPod and cut the sides out of it, the iPhone fits with cases on it just fine. The reason is that the Classic is thicker than the iPhone and accommodates the thickness of the case in this way.
But no, if you're using a 3G/3GS dock that accepts the phone without a case only, it's not going to work right with the iFrogz case on it.