I share the awe of RF (especially as they look naive, but turn out to be extremely good for a wide range of problems), however, the main problem is that they are black boxes. Typically, it is easy to get good results, but almost no insight, or further pointers.

Many times I ended up using linear regression (with properly engineered variables), or something as simple, because it gave almost as good results as RF, but I could interpret the results, inputs, etc. (And may task was academic or business analytics, so CV score was not the only figure of merit.)