Took me awhile to figure this out myself. Like slider said, you have to find a land "low point", move your transport next to it, select the troop in the boat and then right click to the land square you want to unload at. The trick is trying to identify "low points" on the cloth map (since the 3D map for me is so slow I'm afraid to go to that view in fear of a freeze or crash hehe).

Thanks! I spent alot of time in the beginning unable to use valuable units. It kinda blows though. You're limited where you can land so it's difficult to make effective use of amphibious assault. I supoose on the flip side you can predict where you may be attacked. Have you run across any warships yet?

Yes I agree the A.I. is weak with transports and colonizing with transports is much safer then doing it over land.