I am the developer of qgis flowmapper plugin. I would be please to answer any questions regarding the plugin.
A readme and tutorial data is already included within the zip file that you have downloaded either from the plugin repo or from the website www.cempro.tk
Briefly, supply (i) input node coordinates as text file and (ii) flow data matrix as text file in white space deliminated format and plugin generates node2node straight flow lines automatically in shapefile format.
Example: You have 3 nodes, cities a, b and c
(i) Input node coordinates (geographic) text file should appear as;
(ii) Flow matrix (from city to city) text file should appear as;
0 100 200
150 0 350
70 140 0
Flow mapper is tested to be working in Windows only. It would probably cause error in MacOS or Linux due to slashes in the file paths. But if you are on Windows, you will not face any problems.