Simulink isn't the way to go for small projects with a low budget: a MATLAB license is rather expensive: like the additional packages that may be required for testing on dedicated hardware. It is suited for big projects with a large number of developers working on them. A skilled C developer can write code for simple to trivial projects in a much shorter time than by dragging blocks in Simulink.

MATLAB and Simulink are targeted specifically to engineering and scientific applications; they aren't general-purpose-programming tools. It's difficult, though not impossible, to develop desktop applications or web services using Simulink.

Finally, it's hard to track model changes with software versioning and revision control systems (such as CVS, SVN, Git, Bazaar, or Mercurial). While, to a certain degree, it is possible to spot the differences when saving models with the .mdl format (because it's a structured text file), this has become difficult with the .slx format (a zipped archive with more information on the model). To see and highlight the differences between two versions of the same model, separate software has to be purchased.