Thats how ES planned it in the beginning, but they made multiple types of boats instead of using one boat for everything.
The boats work more like they used to in AoE, you have a Galleon boat (one that attacks using arrows and flaming arrows.), a transport, now you have a melee boat (attacks using big spike on the front.)fishing boat, etc.
If you have played AoE you shouldn't be thrown off by naval units.