CFDTool features a simplified GUI interface to easily get started with fluid mechanics simulations without having to learn PDE equations. CFDTool is also optimized for 1D and 2D simulations.
In contrast the FEATool Multiphysics toolbox is more advanced and allows customizing or entering your own PDEs, as well as arbitrary multiphysics couplings such as fluid-structure interaction (CFDTool is limited to fluid flow <-> heat transfer couplings), and command line scripting.
To sum up, CFDTool is good for beginning to learn CFD simulations, while FEATool offers more features for advanced and power users who want to customize their simulations in some way (CFDTool model files can be seamlessly imported in to FEATool and extended with more multi-physics modes).
