mmm well put it this way, there are the five major countries who have Hidden Villages which are in a sense their army. Fire Country has Hidden Leaf and so on. These villages fund themselfs so far as we know through clients who pay the Hidden villages. Of coz we all know abt the mission ranks right? We assume that most of the funding comes from the high paying missions like S or A ranked but are few n far between where as the lower ranks like D rank are low pay but more in number. Of coz we never see the gov'ts of the countries coz the anime series does actually focus round the Hidden Villages.