I've used Meshcam quite a bit, but never used Madcam. Madcam appears to only work with Rhino, as it's a plug-in , so I'm not sure about STL files.
Meshcam was developed as an easy CAM system for 3D profiling. It is probably one of the easiest CNC programs I've used and it is very affordable. It produces very good toolpaths, but you are limited in choosing the areas to machine. For the most part it is limited to machining the entire surface of a part without giving you the ability to select specific surfaces to cut. It does that job very well and a great way to get started. However, Madcam had more options and since you have Rhino, it's probably a better tool for you.
Rgds,
--Colin--